rs925910

Variant names:

• chr2-35683934-G-A
• rs925910

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 0.405 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.180 AC: 7449 AN: 41486

American (AMR) AF: 0.477 AC: 7275 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.553 AC: 1917 AN: 3468

East Asian (EAS) AF: 0.0709 AC: 367 AN: 5176

South Asian (SAS) AF: 0.311 AC: 1493 AN: 4804

European-Finnish (FIN) AF: 0.444 AC: 4674 AN: 10534

Middle Eastern (MID) AF: 0.596 AC: 174 AN: 292

European-Non Finnish (NFE) AF: 0.542 AC: 36816 AN: 67960

Other (OTH) AF: 0.446 AC: 941 AN: 2110

Alfa AF: 0.507 Hom.: 33282

Bravo AF: 0.398

Asia WGS AF: 0.215 AC: 751 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.1
DANN	Benign	0.57
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs925910; hg19: chr2-35909000;