rs2925216

Variant names:

• chr2-137775186-T-C
• rs2925216

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 0.82 in 151,928 control chromosomes in the GnomAD database, including 52,743 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 (52743 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.234

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• 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: 0.821 AC: 124570 AN: 151810 Hom.: 52709 Cov.: 32

Gnomad AFR AF: 0.655

Gnomad AMI AF: 0.945

Gnomad AMR AF: 0.754

Gnomad ASJ AF: 0.871

Gnomad EAS AF: 0.437

Gnomad SAS AF: 0.783

Gnomad FIN AF: 0.959

Gnomad MID AF: 0.858

Gnomad NFE AF: 0.942

Gnomad OTH AF: 0.805

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

GnomAD4 genome AF: 0.820 AC: 124655 AN: 151928 Hom.: 52743 Cov.: 32 AF XY: 0.818 AC XY: 60724 AN XY: 74248

Gnomad4 AFR AF: 0.656

Gnomad4 AMR AF: 0.754

Gnomad4 ASJ AF: 0.871

Gnomad4 EAS AF: 0.436

Gnomad4 SAS AF: 0.783

Gnomad4 FIN AF: 0.959

Gnomad4 NFE AF: 0.942

Gnomad4 OTH AF: 0.806

Alfa AF: 0.854 Hom.: 8938

Bravo AF: 0.793

Asia WGS AF: 0.646 AC: 2247 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.92
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2925216; hg19: chr2-138532756; COSMIC: COSV70042900;