rs1424760

chr2-162925277-C-T

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;