11-37862767-A-T

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 0.957 in 152,292 control chromosomes in the GnomAD database, including 69,899 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 0.96 (69899 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.735

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.986 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.957 AC: 145626 AN: 152174 Hom.: 69863 Cov.: 33

Gnomad AFR AF: 0.888

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.950

Gnomad ASJ AF: 0.995

Gnomad EAS AF: 0.993

Gnomad SAS AF: 0.969

Gnomad FIN AF: 0.969

Gnomad MID AF: 0.975

Gnomad NFE AF: 0.992

Gnomad OTH AF: 0.967

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

GnomAD4 genome AF: 0.957 AC: 145718 AN: 152292 Hom.: 69899 Cov.: 33 AF XY: 0.956 AC XY: 71175 AN XY: 74460

Gnomad4 AFR AF: 0.888

Gnomad4 AMR AF: 0.950

Gnomad4 ASJ AF: 0.995

Gnomad4 EAS AF: 0.993

Gnomad4 SAS AF: 0.969

Gnomad4 FIN AF: 0.969

Gnomad4 NFE AF: 0.992

Gnomad4 OTH AF: 0.967

Alfa AF: 0.965 Hom.: 8808

Bravo AF: 0.953

Asia WGS AF: 0.971 AC: 3375 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.35
Dann	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs963123; hg19: chr11-37884317;