11-81608790-T-C

Variant names:

• chr11-81608790-T-C
• rs1945642

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.412

Gnomad4 AMR AF: 0.716

Gnomad4 ASJ AF: 0.717

Gnomad4 EAS AF: 0.983

Gnomad4 SAS AF: 0.816

Gnomad4 FIN AF: 0.741

Gnomad4 NFE AF: 0.659

Gnomad4 OTH AF: 0.665

Alfa AF: 0.624 Hom.: 3621

Bravo AF: 0.612

Asia WGS AF: 0.862 AC: 2998 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

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