rs2925215

Positions:

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

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 0.922 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.834

Gnomad4 AMR AF: 0.939

Gnomad4 ASJ AF: 0.900

Gnomad4 EAS AF: 0.877

Gnomad4 SAS AF: 0.943

Gnomad4 FIN AF: 0.982

Gnomad4 NFE AF: 0.966

Gnomad4 OTH AF: 0.909

Alfa AF: 0.950 Hom.: 29800

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2925215; hg19: chr2-138533519;