11-38767065-T-C

Variant names:

• chr11-38767065-T-C
• rs11034952

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 0.617 in 152,012 control chromosomes in the GnomAD database, including 29,259 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 0.62 (29259 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.857
• Publications: 7 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 = 0.732 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: 0.617 AC: 93706 AN: 151896 Hom.: 29257 Cov.: 32

Gnomad AFR AF: 0.623

Gnomad AMI AF: 0.447

Gnomad AMR AF: 0.722

Gnomad ASJ AF: 0.677

Gnomad EAS AF: 0.752

Gnomad SAS AF: 0.675

Gnomad FIN AF: 0.525

Gnomad MID AF: 0.753

Gnomad NFE AF: 0.586

Gnomad OTH AF: 0.678

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

GnomAD4 genome AF: 0.617 AC: 93747 AN: 152012 Hom.: 29259 Cov.: 32 AF XY: 0.618 AC XY: 45888 AN XY: 74302

African (AFR) AF: 0.622 AC: 25792 AN: 41460

American (AMR) AF: 0.722 AC: 11008 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.677 AC: 2348 AN: 3470

East Asian (EAS) AF: 0.751 AC: 3881 AN: 5166

South Asian (SAS) AF: 0.676 AC: 3258 AN: 4822

European-Finnish (FIN) AF: 0.525 AC: 5542 AN: 10556

Middle Eastern (MID) AF: 0.745 AC: 219 AN: 294

European-Non Finnish (NFE) AF: 0.586 AC: 39854 AN: 67968

Other (OTH) AF: 0.680 AC: 1438 AN: 2114

Alfa AF: 0.603 Hom.: 49082

Bravo AF: 0.634

Asia WGS AF: 0.719 AC: 2499 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	0.39
DANN	Benign	0.44
PhyloP100		-0.86

Splicing

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

Other links and lift over

dbSNP: rs11034952; hg19: chr11-38788615; COSMIC: COSV99805384;