chr11-62899134-T-G

Variant names:

• chr11-62899134-T-G
• rs2507821

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 0.371 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
• Publications: 8 publications found

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.331 AC: 13683 AN: 41304

American (AMR) AF: 0.315 AC: 4792 AN: 15206

Ashkenazi Jewish (ASJ) AF: 0.359 AC: 1247 AN: 3470

East Asian (EAS) AF: 0.484 AC: 2487 AN: 5140

South Asian (SAS) AF: 0.500 AC: 2396 AN: 4792

European-Finnish (FIN) AF: 0.371 AC: 3876 AN: 10446

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.391 AC: 26569 AN: 67890

Other (OTH) AF: 0.373 AC: 784 AN: 2102

Alfa AF: 0.379 Hom.: 32987

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
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs2507821; hg19: chr11-62666606;