2-136751454-T-G

Variant names:

• chr2-136751454-T-G
• rs10496753

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 0.112 in 152,298 control chromosomes in the GnomAD database, including 1,434 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 0.11 (1434 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.721
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.38 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: 0.112 AC: 17015 AN: 152180 Hom.: 1434 Cov.: 33

Gnomad AFR AF: 0.0435

Gnomad AMI AF: 0.0724

Gnomad AMR AF: 0.187

Gnomad ASJ AF: 0.130

Gnomad EAS AF: 0.395

Gnomad SAS AF: 0.217

Gnomad FIN AF: 0.170

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.0975

Gnomad OTH AF: 0.126

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

GnomAD4 genome AF: 0.112 AC: 17026 AN: 152298 Hom.: 1434 Cov.: 33 AF XY: 0.119 AC XY: 8868 AN XY: 74462

African (AFR) AF: 0.0437 AC: 1817 AN: 41582

American (AMR) AF: 0.187 AC: 2858 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.130 AC: 453 AN: 3472

East Asian (EAS) AF: 0.395 AC: 2044 AN: 5178

South Asian (SAS) AF: 0.218 AC: 1049 AN: 4822

European-Finnish (FIN) AF: 0.170 AC: 1797 AN: 10600

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.0975 AC: 6634 AN: 68022

Other (OTH) AF: 0.124 AC: 263 AN: 2114

Alfa AF: 0.100 Hom.: 192

Bravo AF: 0.111

Asia WGS AF: 0.315 AC: 1093 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	15
DANN	Benign	0.68
PhyloP100		0.72

Splicing

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

Other links and lift over

dbSNP: rs10496753; hg19: chr2-137509024;