rs834830

Positions:

• chr2-156346748-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 0.717 in 152,114 control chromosomes in the GnomAD database, including 39,637 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 0.72 (39637 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.986

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.777 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: 0.717 AC: 109014 AN: 151996 Hom.: 39626 Cov.: 32

Gnomad AFR AF: 0.659

Gnomad AMI AF: 0.771

Gnomad AMR AF: 0.616

Gnomad ASJ AF: 0.774

Gnomad EAS AF: 0.463

Gnomad SAS AF: 0.672

Gnomad FIN AF: 0.787

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.783

Gnomad OTH AF: 0.725

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

GnomAD4 genome AF: 0.717 AC: 109065 AN: 152114 Hom.: 39637 Cov.: 32 AF XY: 0.714 AC XY: 53102 AN XY: 74386

Gnomad4 AFR AF: 0.659

Gnomad4 AMR AF: 0.615

Gnomad4 ASJ AF: 0.774

Gnomad4 EAS AF: 0.463

Gnomad4 SAS AF: 0.673

Gnomad4 FIN AF: 0.787

Gnomad4 NFE AF: 0.783

Gnomad4 OTH AF: 0.725

Alfa AF: 0.757 Hom.: 40110

Bravo AF: 0.695

Asia WGS AF: 0.613 AC: 2132 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.089
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs834830; hg19: chr2-157203260;