rs1424760

Variant names:

• chr2-162925277-C-T
• rs1424760
• ENST00000724875.1:n.342-10367G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000724875.1(ENSG00000294636):​n.342-10367G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000294636 ENST00000724875.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.91
• Publications: 10 publications found

Genes affected

ENSG00000294636 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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
ENSG00000294636	ENST00000724875.1	n.342-10367G>A		intron_variant	Intron 2 of 4

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

African (AFR) AF: 0.243 AC: 10032 AN: 41356

American (AMR) AF: 0.568 AC: 8633 AN: 15210

Ashkenazi Jewish (ASJ) AF: 0.575 AC: 1993 AN: 3468

East Asian (EAS) AF: 0.464 AC: 2392 AN: 5152

South Asian (SAS) AF: 0.814 AC: 3923 AN: 4818

European-Finnish (FIN) AF: 0.619 AC: 6501 AN: 10504

Middle Eastern (MID) AF: 0.673 AC: 198 AN: 294

European-Non Finnish (NFE) AF: 0.650 AC: 44171 AN: 67924

Other (OTH) AF: 0.546 AC: 1151 AN: 2108

Alfa AF: 0.607 Hom.: 105174

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
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs1424760; hg19: chr2-163781787;