rs2925215

Variant names:

• chr2-137775949-T-C
• rs2925215

Your query was ambiguous. Multiple possible variants found:

• chr2-137775949-T-C
• chr2-137775949-T-G

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 0.922 in 151,918 control chromosomes in the GnomAD database, including 64,866 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 0.92 (64866 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.814
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.96 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: 0.922 AC: 140031 AN: 151800 Hom.: 64816 Cov.: 30

Gnomad AFR AF: 0.834

Gnomad AMI AF: 0.987

Gnomad AMR AF: 0.939

Gnomad ASJ AF: 0.900

Gnomad EAS AF: 0.877

Gnomad SAS AF: 0.943

Gnomad FIN AF: 0.982

Gnomad MID AF: 0.920

Gnomad NFE AF: 0.966

Gnomad OTH AF: 0.909

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

GnomAD4 genome AF: 0.922 AC: 140140 AN: 151918 Hom.: 64866 Cov.: 30 AF XY: 0.924 AC XY: 68624 AN XY: 74260

African (AFR) AF: 0.834 AC: 34598 AN: 41464

American (AMR) AF: 0.939 AC: 14318 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.900 AC: 3124 AN: 3470

East Asian (EAS) AF: 0.877 AC: 4494 AN: 5124

South Asian (SAS) AF: 0.943 AC: 4539 AN: 4812

European-Finnish (FIN) AF: 0.982 AC: 10418 AN: 10610

Middle Eastern (MID) AF: 0.924 AC: 268 AN: 290

European-Non Finnish (NFE) AF: 0.966 AC: 65563 AN: 67882

Other (OTH) AF: 0.909 AC: 1920 AN: 2112

Alfa AF: 0.949 Hom.: 33611

Bravo AF: 0.915

Asia WGS AF: 0.912 AC: 3173 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.41
PhyloP100		-0.81

Splicing

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

Other links and lift over

dbSNP: rs2925215; hg19: chr2-138533519;