rs694510

Positions:

• chr2-136523291-G-T

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;