rs2846236

chr11-124195920-G-A

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 0.557 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.520

Gnomad4 AMR AF: 0.586

Gnomad4 ASJ AF: 0.549

Gnomad4 EAS AF: 0.637

Gnomad4 SAS AF: 0.433

Gnomad4 FIN AF: 0.611

Gnomad4 NFE AF: 0.571

Gnomad4 OTH AF: 0.562

Alfa AF: 0.568 Hom.: 41226

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2846236; hg19: chr11-124066627;