6-32786304-T-C

Variant names:

• chr6-32786304-T-C
• rs2261566

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.646 in 151,908 control chromosomes in the GnomAD database, including 31,817 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.65 (31817 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.176
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.716 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.646 AC: 98095 AN: 151790 Hom.: 31796 Cov.: 31

Gnomad AFR AF: 0.650

Gnomad AMI AF: 0.760

Gnomad AMR AF: 0.623

Gnomad ASJ AF: 0.649

Gnomad EAS AF: 0.735

Gnomad SAS AF: 0.723

Gnomad FIN AF: 0.700

Gnomad MID AF: 0.650

Gnomad NFE AF: 0.628

Gnomad OTH AF: 0.631

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.646 AC: 98160 AN: 151908 Hom.: 31817 Cov.: 31 AF XY: 0.650 AC XY: 48285 AN XY: 74246

African (AFR) AF: 0.649 AC: 26901 AN: 41426

American (AMR) AF: 0.623 AC: 9517 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.649 AC: 2246 AN: 3462

East Asian (EAS) AF: 0.735 AC: 3795 AN: 5162

South Asian (SAS) AF: 0.723 AC: 3475 AN: 4808

European-Finnish (FIN) AF: 0.700 AC: 7386 AN: 10558

Middle Eastern (MID) AF: 0.668 AC: 195 AN: 292

European-Non Finnish (NFE) AF: 0.628 AC: 42612 AN: 67902

Other (OTH) AF: 0.634 AC: 1340 AN: 2112

Alfa AF: 0.653 Hom.: 28966

Bravo AF: 0.640

Asia WGS AF: 0.740 AC: 2570 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.4
DANN	Benign	0.69
PhyloP100		-0.18

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2261566; hg19: chr6-32754081;