rs592582

Variant names:

• chr2-156916874-T-G
• rs592582

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 0.725 in 149,272 control chromosomes in the GnomAD database, including 42,416 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 0.73 (42416 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.483

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.871 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: 0.725 AC: 108231 AN: 149188 Hom.: 42409 Cov.: 28

Gnomad AFR AF: 0.405

Gnomad AMI AF: 0.874

Gnomad AMR AF: 0.752

Gnomad ASJ AF: 0.879

Gnomad EAS AF: 0.830

Gnomad SAS AF: 0.805

Gnomad FIN AF: 0.827

Gnomad MID AF: 0.793

Gnomad NFE AF: 0.877

Gnomad OTH AF: 0.732

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

GnomAD4 genome AF: 0.725 AC: 108259 AN: 149272 Hom.: 42416 Cov.: 28 AF XY: 0.725 AC XY: 52740 AN XY: 72720

Gnomad4 AFR AF: 0.405

Gnomad4 AMR AF: 0.753

Gnomad4 ASJ AF: 0.879

Gnomad4 EAS AF: 0.830

Gnomad4 SAS AF: 0.805

Gnomad4 FIN AF: 0.827

Gnomad4 NFE AF: 0.877

Gnomad4 OTH AF: 0.734

Alfa AF: 0.798 Hom.: 6300

Bravo AF: 0.708

Asia WGS AF: 0.774 AC: 2658 AN: 3438

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	7.9
DANN	Benign	0.90

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs592582; hg19: chr2-157773386;