11-62335948-T-C

Position:

• chr11-62335948-T-C

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 0.891 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.871

Gnomad4 AMR AF: 0.922

Gnomad4 ASJ AF: 0.879

Gnomad4 EAS AF: 0.998

Gnomad4 SAS AF: 0.932

Gnomad4 FIN AF: 0.934

Gnomad4 NFE AF: 0.880

Gnomad4 OTH AF: 0.893

Alfa AF: 0.882 Hom.: 76729

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2463822; hg19: chr11-62103420;