rs10496749

Variant names:

• chr2-136548407-T-C
• rs10496749
• ENST00000803876.1:n.161-1702A>G

Your query was ambiguous. Multiple possible variants found:

• chr2-136548407-T-C
• chr2-136548407-T-G

Variant summary

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

The ENST00000803876.1(ENSG00000304503):​n.161-1702A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.172 in 152,074 control chromosomes in the GnomAD database, including 2,649 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 0.17 (2649 hom., cov: 32)
• Consequence: ENSG00000304503 ENST00000803876.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.54
• Publications: 3 publications found

Genes affected

ENSG00000304503 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.401 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105373633	XR_923360.3	n.202-1702A>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000304503	ENST00000803876.1	n.161-1702A>G		intron_variant	Intron 1 of 3
ENSG00000304503	ENST00000803877.1	n.158-3503A>G		intron_variant	Intron 1 of 2
ENSG00000304503	ENST00000803878.1	n.242-1702A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.172 AC: 26169 AN: 151956 Hom.: 2645 Cov.: 32

Gnomad AFR AF: 0.149

Gnomad AMI AF: 0.102

Gnomad AMR AF: 0.293

Gnomad ASJ AF: 0.155

Gnomad EAS AF: 0.415

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.183

Gnomad MID AF: 0.239

Gnomad NFE AF: 0.136

Gnomad OTH AF: 0.187

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

GnomAD4 genome AF: 0.172 AC: 26191 AN: 152074 Hom.: 2649 Cov.: 32 AF XY: 0.179 AC XY: 13326 AN XY: 74328

African (AFR) AF: 0.149 AC: 6197 AN: 41482

American (AMR) AF: 0.294 AC: 4492 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.155 AC: 539 AN: 3470

East Asian (EAS) AF: 0.416 AC: 2143 AN: 5156

South Asian (SAS) AF: 0.223 AC: 1075 AN: 4820

European-Finnish (FIN) AF: 0.183 AC: 1937 AN: 10576

Middle Eastern (MID) AF: 0.233 AC: 68 AN: 292

European-Non Finnish (NFE) AF: 0.136 AC: 9256 AN: 67984

Other (OTH) AF: 0.186 AC: 392 AN: 2110

Alfa AF: 0.0816 Hom.: 126

Bravo AF: 0.183

Asia WGS AF: 0.319 AC: 1108 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.8
DANN	Benign	0.53
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs10496749; hg19: chr2-137305977;