chr2-136585238-G-A

Variant names:

• chr2-136585238-G-A
• rs10496750

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 0.646 in 152,042 control chromosomes in the GnomAD database, including 34,995 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 0.65 (34995 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.740
• Publications: 3 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 = 0.795 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: 0.646 AC: 98192 AN: 151930 Hom.: 35001 Cov.: 32

Gnomad AFR AF: 0.330

Gnomad AMI AF: 0.905

Gnomad AMR AF: 0.707

Gnomad ASJ AF: 0.517

Gnomad EAS AF: 0.653

Gnomad SAS AF: 0.623

Gnomad FIN AF: 0.836

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.800

Gnomad OTH AF: 0.633

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

GnomAD4 genome AF: 0.646 AC: 98202 AN: 152042 Hom.: 34995 Cov.: 32 AF XY: 0.648 AC XY: 48170 AN XY: 74328

African (AFR) AF: 0.330 AC: 13646 AN: 41384

American (AMR) AF: 0.707 AC: 10801 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.517 AC: 1794 AN: 3472

East Asian (EAS) AF: 0.653 AC: 3372 AN: 5166

South Asian (SAS) AF: 0.622 AC: 2996 AN: 4814

European-Finnish (FIN) AF: 0.836 AC: 8860 AN: 10592

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.800 AC: 54441 AN: 68018

Other (OTH) AF: 0.628 AC: 1322 AN: 2106

Alfa AF: 0.729 Hom.: 52785

Bravo AF: 0.624

Asia WGS AF: 0.587 AC: 2042 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	0.88
DANN	Benign	0.65
PhyloP100		-0.74

Splicing

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

Other links and lift over

dbSNP: rs10496750; hg19: chr2-137342808;