2-136461372-T-C

Variant names:

• chr2-136461372-T-C
• rs938359

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 0.291 in 152,084 control chromosomes in the GnomAD database, including 8,426 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 0.29 (8426 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.545
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.502 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.290 AC: 44093 AN: 151966 Hom.: 8397 Cov.: 32

Gnomad AFR AF: 0.508

Gnomad AMI AF: 0.106

Gnomad AMR AF: 0.353

Gnomad ASJ AF: 0.223

Gnomad EAS AF: 0.514

Gnomad SAS AF: 0.270

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.278

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

GnomAD4 genome AF: 0.291 AC: 44189 AN: 152084 Hom.: 8426 Cov.: 32 AF XY: 0.295 AC XY: 21915 AN XY: 74362

African (AFR) AF: 0.508 AC: 21055 AN: 41446

American (AMR) AF: 0.353 AC: 5398 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.223 AC: 774 AN: 3470

East Asian (EAS) AF: 0.515 AC: 2666 AN: 5178

South Asian (SAS) AF: 0.269 AC: 1300 AN: 4824

European-Finnish (FIN) AF: 0.190 AC: 2008 AN: 10574

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.150 AC: 10208 AN: 67994

Other (OTH) AF: 0.281 AC: 593 AN: 2108

Alfa AF: 0.243 Hom.: 779

Bravo AF: 0.316

Asia WGS AF: 0.399 AC: 1384 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
DANN	Benign	0.72
PhyloP100		-0.55

Splicing

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

Other links and lift over

dbSNP: rs938359; hg19: chr2-137218942;