6-32411163-C-T

Variant names:

• chr6-32411163-C-T
• rs3129961

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 0.718 in 152,000 control chromosomes in the GnomAD database, including 39,345 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 0.72 (39345 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.180
• Publications: 19 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.763 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.718 AC: 109042 AN: 151884 Hom.: 39325 Cov.: 31

Gnomad AFR AF: 0.770

Gnomad AMI AF: 0.779

Gnomad AMR AF: 0.691

Gnomad ASJ AF: 0.696

Gnomad EAS AF: 0.731

Gnomad SAS AF: 0.710

Gnomad FIN AF: 0.755

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.687

Gnomad OTH AF: 0.721

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

GnomAD4 genome AF: 0.718 AC: 109106 AN: 152000 Hom.: 39345 Cov.: 31 AF XY: 0.717 AC XY: 53296 AN XY: 74288

African (AFR) AF: 0.770 AC: 31920 AN: 41452

American (AMR) AF: 0.691 AC: 10560 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.696 AC: 2411 AN: 3466

East Asian (EAS) AF: 0.732 AC: 3781 AN: 5166

South Asian (SAS) AF: 0.710 AC: 3419 AN: 4818

European-Finnish (FIN) AF: 0.755 AC: 7987 AN: 10572

Middle Eastern (MID) AF: 0.554 AC: 163 AN: 294

European-Non Finnish (NFE) AF: 0.687 AC: 46650 AN: 67944

Other (OTH) AF: 0.715 AC: 1506 AN: 2106

Alfa AF: 0.695 Hom.: 110097

Bravo AF: 0.721

Asia WGS AF: 0.717 AC: 2496 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.4
DANN	Benign	0.57
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs3129961; hg19: chr6-32378940;