11-62335948-T-C

Variant names:

• chr11-62335948-T-C
• rs2463822

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 0.891 in 152,230 control chromosomes in the GnomAD database, including 60,528 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 0.89 (60528 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20
• Publications: 25 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 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: 0.891 AC: 135572 AN: 152112 Hom.: 60478 Cov.: 32

Gnomad AFR AF: 0.871

Gnomad AMI AF: 0.901

Gnomad AMR AF: 0.922

Gnomad ASJ AF: 0.879

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.933

Gnomad FIN AF: 0.934

Gnomad MID AF: 0.883

Gnomad NFE AF: 0.880

Gnomad OTH AF: 0.892

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

GnomAD4 genome AF: 0.891 AC: 135681 AN: 152230 Hom.: 60528 Cov.: 32 AF XY: 0.895 AC XY: 66634 AN XY: 74420

African (AFR) AF: 0.871 AC: 36167 AN: 41532

American (AMR) AF: 0.922 AC: 14100 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.879 AC: 3051 AN: 3472

East Asian (EAS) AF: 0.998 AC: 5155 AN: 5164

South Asian (SAS) AF: 0.932 AC: 4500 AN: 4826

European-Finnish (FIN) AF: 0.934 AC: 9910 AN: 10608

Middle Eastern (MID) AF: 0.888 AC: 261 AN: 294

European-Non Finnish (NFE) AF: 0.880 AC: 59828 AN: 68020

Other (OTH) AF: 0.893 AC: 1887 AN: 2112

Alfa AF: 0.885 Hom.: 186408

Bravo AF: 0.890

Asia WGS AF: 0.961 AC: 3343 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	1.2
DANN	Benign	0.36
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs2463822; hg19: chr11-62103420;