rs694510

Variant names:

• chr2-136523291-G-T
• rs694510

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 0.355 in 151,998 control chromosomes in the GnomAD database, including 10,308 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 0.35 (10308 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.143
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.527 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.355 AC: 53862 AN: 151880 Hom.: 10284 Cov.: 32

Gnomad AFR AF: 0.433

Gnomad AMI AF: 0.171

Gnomad AMR AF: 0.429

Gnomad ASJ AF: 0.502

Gnomad EAS AF: 0.544

Gnomad SAS AF: 0.479

Gnomad FIN AF: 0.291

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.269

Gnomad OTH AF: 0.401

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

GnomAD4 genome AF: 0.355 AC: 53938 AN: 151998 Hom.: 10308 Cov.: 32 AF XY: 0.361 AC XY: 26836 AN XY: 74298

African (AFR) AF: 0.433 AC: 17950 AN: 41428

American (AMR) AF: 0.429 AC: 6559 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.502 AC: 1740 AN: 3468

East Asian (EAS) AF: 0.544 AC: 2814 AN: 5174

South Asian (SAS) AF: 0.480 AC: 2315 AN: 4822

European-Finnish (FIN) AF: 0.291 AC: 3076 AN: 10568

Middle Eastern (MID) AF: 0.568 AC: 167 AN: 294

European-Non Finnish (NFE) AF: 0.269 AC: 18308 AN: 67956

Other (OTH) AF: 0.407 AC: 853 AN: 2098

Alfa AF: 0.321 Hom.: 1064

Bravo AF: 0.367

Asia WGS AF: 0.543 AC: 1887 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.73
DANN	Benign	0.48
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs694510; hg19: chr2-137280861;