11-124195920-G-A

Variant names:

• chr11-124195920-G-A
• rs2846236

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 0.557 in 151,844 control chromosomes in the GnomAD database, including 23,687 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 0.56 (23687 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.568
• Publications: 2 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 = 0.619 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: 0.557 AC: 84563 AN: 151726 Hom.: 23661 Cov.: 32

Gnomad AFR AF: 0.520

Gnomad AMI AF: 0.431

Gnomad AMR AF: 0.585

Gnomad ASJ AF: 0.549

Gnomad EAS AF: 0.636

Gnomad SAS AF: 0.432

Gnomad FIN AF: 0.611

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.571

Gnomad OTH AF: 0.560

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

GnomAD4 genome AF: 0.557 AC: 84645 AN: 151844 Hom.: 23687 Cov.: 32 AF XY: 0.559 AC XY: 41490 AN XY: 74180

African (AFR) AF: 0.520 AC: 21513 AN: 41374

American (AMR) AF: 0.586 AC: 8930 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.549 AC: 1905 AN: 3470

East Asian (EAS) AF: 0.637 AC: 3291 AN: 5168

South Asian (SAS) AF: 0.433 AC: 2083 AN: 4816

European-Finnish (FIN) AF: 0.611 AC: 6423 AN: 10518

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.571 AC: 38757 AN: 67934

Other (OTH) AF: 0.562 AC: 1186 AN: 2110

Alfa AF: 0.563 Hom.: 64170

Bravo AF: 0.556

Asia WGS AF: 0.526 AC: 1824 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.8
DANN	Benign	0.23
PhyloP100		-0.57

Splicing

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

Other links and lift over

dbSNP: rs2846236; hg19: chr11-124066627;