rs2138140

Variant names:

• chr2-136353359-C-A
• rs2138140

Your query was ambiguous. Multiple possible variants found:

• chr2-136353359-C-A
• chr2-136353359-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.116 in 152,086 control chromosomes in the GnomAD database, including 1,882 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 0.12 (1882 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.411

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.273 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: 0.116 AC: 17638 AN: 151968 Hom.: 1876 Cov.: 31

Gnomad AFR AF: 0.278

Gnomad AMI AF: 0.00330

Gnomad AMR AF: 0.126

Gnomad ASJ AF: 0.0619

Gnomad EAS AF: 0.104

Gnomad SAS AF: 0.0576

Gnomad FIN AF: 0.0407

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0368

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.116 AC: 17661 AN: 152086 Hom.: 1882 Cov.: 31 AF XY: 0.115 AC XY: 8548 AN XY: 74350

Gnomad4 AFR AF: 0.278

Gnomad4 AMR AF: 0.127

Gnomad4 ASJ AF: 0.0619

Gnomad4 EAS AF: 0.104

Gnomad4 SAS AF: 0.0570

Gnomad4 FIN AF: 0.0407

Gnomad4 NFE AF: 0.0368

Gnomad4 OTH AF: 0.108

Alfa AF: 0.0329 Hom.: 46

Bravo AF: 0.133

Asia WGS AF: 0.0930 AC: 322 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.88
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2138140; hg19: chr2-137110929;