rs1424760

Variant names:

• chr2-162925277-C-T
• rs1424760

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 0.525 in 151,746 control chromosomes in the GnomAD database, including 23,488 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 0.53 (23488 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.91

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.793 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: 0.525 AC: 79642 AN: 151628 Hom.: 23470 Cov.: 31

Gnomad AFR AF: 0.242

Gnomad AMI AF: 0.769

Gnomad AMR AF: 0.567

Gnomad ASJ AF: 0.575

Gnomad EAS AF: 0.465

Gnomad SAS AF: 0.815

Gnomad FIN AF: 0.619

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.650

Gnomad OTH AF: 0.545

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

GnomAD4 genome AF: 0.525 AC: 79695 AN: 151746 Hom.: 23488 Cov.: 31 AF XY: 0.530 AC XY: 39270 AN XY: 74154

Gnomad4 AFR AF: 0.243

Gnomad4 AMR AF: 0.568

Gnomad4 ASJ AF: 0.575

Gnomad4 EAS AF: 0.464

Gnomad4 SAS AF: 0.814

Gnomad4 FIN AF: 0.619

Gnomad4 NFE AF: 0.650

Gnomad4 OTH AF: 0.546

Alfa AF: 0.628 Hom.: 50994

Bravo AF: 0.499

Asia WGS AF: 0.606 AC: 2109 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.55
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1424760; hg19: chr2-163781787;