rs3759502

Variant names:

• chr13-103068322-G-A
• rs3759502

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 0.351 in 151,728 control chromosomes in the GnomAD database, including 9,542 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 (9542 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.651
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.406 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: 0.351 AC: 53183 AN: 151610 Hom.: 9530 Cov.: 32

Gnomad AFR AF: 0.368

Gnomad AMI AF: 0.270

Gnomad AMR AF: 0.414

Gnomad ASJ AF: 0.315

Gnomad EAS AF: 0.395

Gnomad SAS AF: 0.341

Gnomad FIN AF: 0.363

Gnomad MID AF: 0.309

Gnomad NFE AF: 0.326

Gnomad OTH AF: 0.327

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

GnomAD4 genome AF: 0.351 AC: 53229 AN: 151728 Hom.: 9542 Cov.: 32 AF XY: 0.354 AC XY: 26249 AN XY: 74128

African (AFR) AF: 0.368 AC: 15198 AN: 41344

American (AMR) AF: 0.414 AC: 6325 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.315 AC: 1090 AN: 3464

East Asian (EAS) AF: 0.395 AC: 2025 AN: 5132

South Asian (SAS) AF: 0.342 AC: 1649 AN: 4816

European-Finnish (FIN) AF: 0.363 AC: 3828 AN: 10534

Middle Eastern (MID) AF: 0.298 AC: 87 AN: 292

European-Non Finnish (NFE) AF: 0.326 AC: 22097 AN: 67862

Other (OTH) AF: 0.324 AC: 685 AN: 2112

Alfa AF: 0.342 Hom.: 1147

Bravo AF: 0.359

Asia WGS AF: 0.322 AC: 1121 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	4.8
DANN	Benign	0.55
PhyloP100		0.65

Splicing

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

Other links and lift over

dbSNP: rs3759502; hg19: chr13-103720672;