2-10436298-T-C

Variant names:

• chr2-10436298-T-C
• rs2463463
• ENST00000757451.1:n.251+4054T>C

Variant summary

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

The ENST00000757451.1(ENSG00000298698):​n.251+4054T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.541 in 151,842 control chromosomes in the GnomAD database, including 22,730 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 0.54 (22730 hom., cov: 33)
• Consequence: ENSG00000298698 ENST00000757451.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13
• Publications: 5 publications found

Genes affected

ENSG00000298698 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.563 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
ENSG00000298698	ENST00000757451.1	n.251+4054T>C		intron_variant	Intron 1 of 1
ENSG00000298698	ENST00000757452.1	n.132+4054T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.542 AC: 82174 AN: 151724 Hom.: 22721 Cov.: 33

Gnomad AFR AF: 0.528

Gnomad AMI AF: 0.727

Gnomad AMR AF: 0.402

Gnomad ASJ AF: 0.450

Gnomad EAS AF: 0.387

Gnomad SAS AF: 0.561

Gnomad FIN AF: 0.717

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.568

Gnomad OTH AF: 0.510

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

GnomAD4 genome AF: 0.541 AC: 82216 AN: 151842 Hom.: 22730 Cov.: 33 AF XY: 0.544 AC XY: 40393 AN XY: 74208

African (AFR) AF: 0.528 AC: 21862 AN: 41396

American (AMR) AF: 0.401 AC: 6129 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.450 AC: 1563 AN: 3470

East Asian (EAS) AF: 0.386 AC: 1990 AN: 5152

South Asian (SAS) AF: 0.560 AC: 2703 AN: 4824

European-Finnish (FIN) AF: 0.717 AC: 7550 AN: 10536

Middle Eastern (MID) AF: 0.527 AC: 154 AN: 292

European-Non Finnish (NFE) AF: 0.568 AC: 38535 AN: 67876

Other (OTH) AF: 0.508 AC: 1070 AN: 2106

Alfa AF: 0.564 Hom.: 17926

Bravo AF: 0.512

Asia WGS AF: 0.467 AC: 1625 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.71
DANN	Benign	0.67
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs2463463; hg19: chr2-10576424;