11-37862767-A-T

Variant names:

• chr11-37862767-A-T
• rs963123

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 0.957 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.888 AC: 36891 AN: 41542

American (AMR) AF: 0.950 AC: 14516 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.995 AC: 3456 AN: 3472

East Asian (EAS) AF: 0.993 AC: 5134 AN: 5172

South Asian (SAS) AF: 0.969 AC: 4678 AN: 4830

European-Finnish (FIN) AF: 0.969 AC: 10293 AN: 10622

Middle Eastern (MID) AF: 0.973 AC: 286 AN: 294

European-Non Finnish (NFE) AF: 0.992 AC: 67506 AN: 68046

Other (OTH) AF: 0.967 AC: 2046 AN: 2116

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
PhyloP100		-0.73

Splicing

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

Other links and lift over

dbSNP: rs963123; hg19: chr11-37884317;