chr11-32874118-T-C

Variant names:

• chr11-32874118-T-C
• rs10767971

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 0.642 in 152,062 control chromosomes in the GnomAD database, including 31,718 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 0.64 (31718 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.114
• Publications: 20 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 (SAS) allele frequency at 95% confidence interval = 0.727 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: 0.642 AC: 97510 AN: 151944 Hom.: 31666 Cov.: 32

Gnomad AFR AF: 0.721

Gnomad AMI AF: 0.589

Gnomad AMR AF: 0.629

Gnomad ASJ AF: 0.563

Gnomad EAS AF: 0.458

Gnomad SAS AF: 0.747

Gnomad FIN AF: 0.713

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.598

Gnomad OTH AF: 0.596

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

GnomAD4 genome AF: 0.642 AC: 97618 AN: 152062 Hom.: 31718 Cov.: 32 AF XY: 0.650 AC XY: 48272 AN XY: 74310

African (AFR) AF: 0.721 AC: 29917 AN: 41488

American (AMR) AF: 0.630 AC: 9618 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.563 AC: 1955 AN: 3470

East Asian (EAS) AF: 0.459 AC: 2370 AN: 5166

South Asian (SAS) AF: 0.747 AC: 3607 AN: 4826

European-Finnish (FIN) AF: 0.713 AC: 7531 AN: 10558

Middle Eastern (MID) AF: 0.582 AC: 171 AN: 294

European-Non Finnish (NFE) AF: 0.598 AC: 40650 AN: 67966

Other (OTH) AF: 0.598 AC: 1264 AN: 2114

Alfa AF: 0.611 Hom.: 101932

Bravo AF: 0.635

Asia WGS AF: 0.595 AC: 2072 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	2.1
DANN	Benign	0.32
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs10767971; hg19: chr11-32895664;