rs2925216

chr2-137775186-T-C

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;