11-81608790-T-C

Variant names:

• chr11-81608790-T-C
• rs1945642

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 0.62 in 151,964 control chromosomes in the GnomAD database, including 30,888 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 (30888 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.499
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.96 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: 0.621 AC: 94231 AN: 151846 Hom.: 30870 Cov.: 31

Gnomad AFR AF: 0.412

Gnomad AMI AF: 0.592

Gnomad AMR AF: 0.716

Gnomad ASJ AF: 0.717

Gnomad EAS AF: 0.983

Gnomad SAS AF: 0.815

Gnomad FIN AF: 0.741

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.659

Gnomad OTH AF: 0.661

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

GnomAD4 genome AF: 0.620 AC: 94275 AN: 151964 Hom.: 30888 Cov.: 31 AF XY: 0.631 AC XY: 46873 AN XY: 74244

African (AFR) AF: 0.412 AC: 17052 AN: 41410

American (AMR) AF: 0.716 AC: 10932 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.717 AC: 2489 AN: 3470

East Asian (EAS) AF: 0.983 AC: 5073 AN: 5162

South Asian (SAS) AF: 0.816 AC: 3929 AN: 4816

European-Finnish (FIN) AF: 0.741 AC: 7833 AN: 10564

Middle Eastern (MID) AF: 0.755 AC: 222 AN: 294

European-Non Finnish (NFE) AF: 0.659 AC: 44801 AN: 67964

Other (OTH) AF: 0.665 AC: 1405 AN: 2114

Alfa AF: 0.616 Hom.: 3691

Bravo AF: 0.612

Asia WGS AF: 0.862 AC: 2998 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.60
DANN	Benign	0.42
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs1945642; hg19: chr11-81319832; COSMIC: COSV53395890;