rs694510

Variant names:

• chr2-136523291-G-T
• rs694510

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 0.355 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.355 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

Gnomad4 AFR AF: 0.433

Gnomad4 AMR AF: 0.429

Gnomad4 ASJ AF: 0.502

Gnomad4 EAS AF: 0.544

Gnomad4 SAS AF: 0.480

Gnomad4 FIN AF: 0.291

Gnomad4 NFE AF: 0.269

Gnomad4 OTH AF: 0.407

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs694510; hg19: chr2-137280861;