chr2-136531577-T-C

Variant names:

• chr2-136531577-T-C
• rs876338

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 0.395 in 152,006 control chromosomes in the GnomAD database, including 12,724 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 0.40 (12724 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00700
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.572 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.395 AC: 59997 AN: 151888 Hom.: 12696 Cov.: 32

Gnomad AFR AF: 0.476

Gnomad AMI AF: 0.187

Gnomad AMR AF: 0.460

Gnomad ASJ AF: 0.529

Gnomad EAS AF: 0.590

Gnomad SAS AF: 0.556

Gnomad FIN AF: 0.323

Gnomad MID AF: 0.637

Gnomad NFE AF: 0.310

Gnomad OTH AF: 0.440

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

GnomAD4 genome AF: 0.395 AC: 60081 AN: 152006 Hom.: 12724 Cov.: 32 AF XY: 0.402 AC XY: 29892 AN XY: 74310

African (AFR) AF: 0.476 AC: 19735 AN: 41436

American (AMR) AF: 0.461 AC: 7041 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.529 AC: 1834 AN: 3466

East Asian (EAS) AF: 0.590 AC: 3045 AN: 5162

South Asian (SAS) AF: 0.557 AC: 2684 AN: 4816

European-Finnish (FIN) AF: 0.323 AC: 3410 AN: 10572

Middle Eastern (MID) AF: 0.640 AC: 187 AN: 292

European-Non Finnish (NFE) AF: 0.310 AC: 21036 AN: 67956

Other (OTH) AF: 0.445 AC: 939 AN: 2112

Alfa AF: 0.364 Hom.: 1658

Bravo AF: 0.406

Asia WGS AF: 0.596 AC: 2071 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.9
DANN	Benign	0.49
PhyloP100		-0.0070

Splicing

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

Other links and lift over

dbSNP: rs876338; hg19: chr2-137289147;