ENST00000762706.1:n.404+25195A>G

Variant names:

• chr2-112796091-A-G
• rs10496444
• ENST00000762706.1:n.404+25195A>G

Variant summary

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

The ENST00000762706.1(ENSG00000299339):​n.404+25195A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.309 in 152,058 control chromosomes in the GnomAD database, including 8,041 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 0.31 (8041 hom., cov: 31)
• Consequence: ENSG00000299339 ENST00000762706.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0510
• Publications: 15 publications found

Genes affected

ENSG00000299339 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.69 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
ENSG00000299339	ENST00000762706.1	n.404+25195A>G		intron_variant	Intron 2 of 3
ENSG00000299339	ENST00000762707.1	n.499+25195A>G		intron_variant	Intron 2 of 2
ENSG00000299339	ENST00000762708.1	n.265+25195A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.309 AC: 46966 AN: 151940 Hom.: 8025 Cov.: 31

Gnomad AFR AF: 0.220

Gnomad AMI AF: 0.232

Gnomad AMR AF: 0.397

Gnomad ASJ AF: 0.268

Gnomad EAS AF: 0.708

Gnomad SAS AF: 0.314

Gnomad FIN AF: 0.402

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.302

Gnomad OTH AF: 0.315

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

GnomAD4 genome AF: 0.309 AC: 47001 AN: 152058 Hom.: 8041 Cov.: 31 AF XY: 0.318 AC XY: 23621 AN XY: 74302

African (AFR) AF: 0.220 AC: 9108 AN: 41472

American (AMR) AF: 0.398 AC: 6082 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.268 AC: 929 AN: 3470

East Asian (EAS) AF: 0.709 AC: 3667 AN: 5174

South Asian (SAS) AF: 0.314 AC: 1516 AN: 4826

European-Finnish (FIN) AF: 0.402 AC: 4238 AN: 10540

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.302 AC: 20513 AN: 67980

Other (OTH) AF: 0.319 AC: 674 AN: 2112

Alfa AF: 0.307 Hom.: 33535

Bravo AF: 0.311

Asia WGS AF: 0.482 AC: 1671 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	4.3
DANN	Benign	0.36
PhyloP100		-0.051

Splicing

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

Other links and lift over

dbSNP: rs10496444; hg19: chr2-113553668; COSMIC: COSV60092694;