rs1580140

Variant names:

• chr2-137811403-T-G
• rs1580140

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 0.815 in 151,996 control chromosomes in the GnomAD database, including 52,247 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 0.82 (52247 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.66
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.936 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: 0.815 AC: 123843 AN: 151878 Hom.: 52232 Cov.: 32

Gnomad AFR AF: 0.637

Gnomad AMI AF: 0.945

Gnomad AMR AF: 0.755

Gnomad ASJ AF: 0.871

Gnomad EAS AF: 0.438

Gnomad SAS AF: 0.782

Gnomad FIN AF: 0.959

Gnomad MID AF: 0.860

Gnomad NFE AF: 0.942

Gnomad OTH AF: 0.798

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

GnomAD4 genome AF: 0.815 AC: 123897 AN: 151996 Hom.: 52247 Cov.: 32 AF XY: 0.813 AC XY: 60392 AN XY: 74306

African (AFR) AF: 0.636 AC: 26373 AN: 41450

American (AMR) AF: 0.755 AC: 11491 AN: 15212

Ashkenazi Jewish (ASJ) AF: 0.871 AC: 3022 AN: 3470

East Asian (EAS) AF: 0.438 AC: 2253 AN: 5146

South Asian (SAS) AF: 0.782 AC: 3775 AN: 4826

European-Finnish (FIN) AF: 0.959 AC: 10174 AN: 10614

Middle Eastern (MID) AF: 0.856 AC: 250 AN: 292

European-Non Finnish (NFE) AF: 0.942 AC: 64013 AN: 67966

Other (OTH) AF: 0.799 AC: 1684 AN: 2108

Alfa AF: 0.861 Hom.: 7491

Bravo AF: 0.787

Asia WGS AF: 0.641 AC: 2234 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.089
DANN	Benign	0.68
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs1580140; hg19: chr2-138568973;