11-62899134-T-G

Position:

• chr11-62899134-T-G

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 0.371 in 151,548 control chromosomes in the GnomAD database, including 10,688 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 0.37 (10688 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.141

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.483 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: 0.371 AC: 56255 AN: 151430 Hom.: 10687 Cov.: 30

Gnomad AFR AF: 0.331

Gnomad AMI AF: 0.344

Gnomad AMR AF: 0.316

Gnomad ASJ AF: 0.359

Gnomad EAS AF: 0.485

Gnomad SAS AF: 0.500

Gnomad FIN AF: 0.371

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.391

Gnomad OTH AF: 0.374

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

GnomAD4 genome AF: 0.371 AC: 56278 AN: 151548 Hom.: 10688 Cov.: 30 AF XY: 0.371 AC XY: 27475 AN XY: 74034

Gnomad4 AFR AF: 0.331

Gnomad4 AMR AF: 0.315

Gnomad4 ASJ AF: 0.359

Gnomad4 EAS AF: 0.484

Gnomad4 SAS AF: 0.500

Gnomad4 FIN AF: 0.371

Gnomad4 NFE AF: 0.391

Gnomad4 OTH AF: 0.373

Alfa AF: 0.380 Hom.: 14846

Bravo AF: 0.365

Asia WGS AF: 0.485 AC: 1689 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.8
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2507821; hg19: chr11-62666606;