rs925910

Variant names:

• chr2-35683934-G-A
• rs925910

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 0.405 in 152,004 control chromosomes in the GnomAD database, including 14,587 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 0.41 (14587 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.485

ACMG classification

Verdict is Benign. Variant got -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 = 0.537 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: 0.406 AC: 61600 AN: 151884 Hom.: 14583 Cov.: 32

Gnomad AFR AF: 0.180

Gnomad AMI AF: 0.564

Gnomad AMR AF: 0.476

Gnomad ASJ AF: 0.553

Gnomad EAS AF: 0.0705

Gnomad SAS AF: 0.310

Gnomad FIN AF: 0.444

Gnomad MID AF: 0.583

Gnomad NFE AF: 0.542

Gnomad OTH AF: 0.449

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

GnomAD4 genome AF: 0.405 AC: 61620 AN: 152004 Hom.: 14587 Cov.: 32 AF XY: 0.398 AC XY: 29543 AN XY: 74256

Gnomad4 AFR AF: 0.180

Gnomad4 AMR AF: 0.477

Gnomad4 ASJ AF: 0.553

Gnomad4 EAS AF: 0.0709

Gnomad4 SAS AF: 0.311

Gnomad4 FIN AF: 0.444

Gnomad4 NFE AF: 0.542

Gnomad4 OTH AF: 0.446

Alfa AF: 0.519 Hom.: 26929

Bravo AF: 0.398

Asia WGS AF: 0.215 AC: 751 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	1.1
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs925910; hg19: chr2-35909000;