rs10496744

Variant names:

• chr2-136401813-G-A
• rs10496744

Variant summary

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

The variant allele was found at a frequency of 0.126 in 152,168 control chromosomes in the GnomAD database, including 1,326 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 0.13 (1326 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.917
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.146 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

Frequencies

GnomAD3 genomes AF: 0.126 AC: 19099 AN: 152050 Hom.: 1328 Cov.: 32

Gnomad AFR AF: 0.105

Gnomad AMI AF: 0.0921

Gnomad AMR AF: 0.0795

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.0396

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.178

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.148

Gnomad OTH AF: 0.101

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

GnomAD4 genome AF: 0.126 AC: 19108 AN: 152168 Hom.: 1326 Cov.: 32 AF XY: 0.125 AC XY: 9302 AN XY: 74400

African (AFR) AF: 0.105 AC: 4349 AN: 41520

American (AMR) AF: 0.0793 AC: 1212 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.134 AC: 465 AN: 3468

East Asian (EAS) AF: 0.0399 AC: 207 AN: 5184

South Asian (SAS) AF: 0.119 AC: 576 AN: 4822

European-Finnish (FIN) AF: 0.178 AC: 1886 AN: 10576

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.148 AC: 10083 AN: 68000

Other (OTH) AF: 0.102 AC: 215 AN: 2106

Alfa AF: 0.136 Hom.: 2569

Bravo AF: 0.115

Asia WGS AF: 0.0840 AC: 290 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.35
DANN	Benign	0.61
PhyloP100		-0.92

Splicing

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

Other links and lift over

dbSNP: rs10496744; hg19: chr2-137159383;