rs10497709

Variant names:

• chr2-190792203-T-C
• rs10497709
• ENST00000676095.2:n.194+23525A>G

Variant summary

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

The ENST00000676095.2(ENSG00000228509):​n.194+23525A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.25 in 152,022 control chromosomes in the GnomAD database, including 5,081 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 0.25 (5081 hom., cov: 31)
• Consequence: ENSG00000228509 ENST00000676095.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.899
• Publications: 5 publications found

Genes affected

ENSG00000228509 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.309 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
ENSG00000228509	ENST00000676095.2	n.194+23525A>G		intron_variant	Intron 2 of 8
ENSG00000228509	ENST00000772360.1	n.285+23525A>G		intron_variant	Intron 2 of 3
ENSG00000228509	ENST00000772361.1	n.180+23525A>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.250 AC: 37954 AN: 151904 Hom.: 5080 Cov.: 31

Gnomad AFR AF: 0.182

Gnomad AMI AF: 0.169

Gnomad AMR AF: 0.225

Gnomad ASJ AF: 0.226

Gnomad EAS AF: 0.102

Gnomad SAS AF: 0.322

Gnomad FIN AF: 0.391

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.284

Gnomad OTH AF: 0.247

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

GnomAD4 genome AF: 0.250 AC: 37974 AN: 152022 Hom.: 5081 Cov.: 31 AF XY: 0.254 AC XY: 18845 AN XY: 74330

African (AFR) AF: 0.182 AC: 7549 AN: 41494

American (AMR) AF: 0.225 AC: 3438 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.226 AC: 783 AN: 3472

East Asian (EAS) AF: 0.101 AC: 524 AN: 5188

South Asian (SAS) AF: 0.322 AC: 1552 AN: 4814

European-Finnish (FIN) AF: 0.391 AC: 4125 AN: 10556

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.284 AC: 19288 AN: 67918

Other (OTH) AF: 0.246 AC: 519 AN: 2108

Alfa AF: 0.260 Hom.: 881

Bravo AF: 0.230

Asia WGS AF: 0.255 AC: 886 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	8.7
DANN	Benign	0.86
PhyloP100		0.90

Splicing

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

Other links and lift over

dbSNP: rs10497709; hg19: chr2-191656929;