Variant: 9:135139901 T / C

Filter Status: PASS
dbSNP: rs1056899
Allele Frequency: 0.3926
Filtering AF: 0.7392 (African)
Allele Count: 47605 / 121252
UCSC: 9-135139901-T-C
ClinVar: Click to search for variant in Clinvar

Genotype Quality Metrics

Note: Plot may include low-quality genotypes that were excluded from allele counts in the table above

Site Quality Metrics

Note: These are site-level quality metrics: they may be unpredictable for multi-allelic sites.

Annotations

This variant falls on 5 transcripts in 1 genes:

missense

SETX

non coding transcript exon

SETX - ENST00000477049

Note: This list may not include additional transcripts in the same gene that the variant does not overlap.

Population Frequencies

Population	Allele Count	Allele Number	Number of Homozygotes	Allele Frequency
European (Non-Finnish)	20213	66662	3090	0.3032
East Asian	6326	8630	2340	0.733
Other	343	906	62	0.3786
African	7822	10386	2948	0.7531
Latino	3595	11558	597	0.311
South Asian	7300	16508	1666	0.4422
European (Finnish)	2006	6602	315	0.3038
Total	47605	121252	11018	0.3926

Read Data

This interactive IGV.js visualization shows reads that went into calling this variant.
Note: These are reassembled reads produced by GATK HaplotypeCaller --bamOutput so they accurately represent what HaplotypeCaller was seeing when it called this variant.