13-103068328-A-T

Variant names:

• chr13-103068328-A-T
• rs3759501

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 151,752 control chromosomes in the GnomAD database, including 9,562 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 (9562 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0770
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• 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: 53216 AN: 151634 Hom.: 9550 Cov.: 32

Gnomad AFR AF: 0.368

Gnomad AMI AF: 0.272

Gnomad AMR AF: 0.414

Gnomad ASJ AF: 0.314

Gnomad EAS AF: 0.395

Gnomad SAS AF: 0.340

Gnomad FIN AF: 0.364

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.326

Gnomad OTH AF: 0.328

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

GnomAD4 genome AF: 0.351 AC: 53262 AN: 151752 Hom.: 9562 Cov.: 32 AF XY: 0.354 AC XY: 26267 AN XY: 74148

African (AFR) AF: 0.368 AC: 15207 AN: 41350

American (AMR) AF: 0.414 AC: 6324 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.314 AC: 1089 AN: 3464

East Asian (EAS) AF: 0.395 AC: 2030 AN: 5142

South Asian (SAS) AF: 0.342 AC: 1644 AN: 4814

European-Finnish (FIN) AF: 0.364 AC: 3838 AN: 10532

Middle Eastern (MID) AF: 0.303 AC: 89 AN: 294

European-Non Finnish (NFE) AF: 0.326 AC: 22106 AN: 67872

Other (OTH) AF: 0.325 AC: 688 AN: 2114

Alfa AF: 0.330 Hom.: 1013

Bravo AF: 0.359

Asia WGS AF: 0.320 AC: 1116 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.5
DANN	Benign	0.55
PhyloP100		-0.077

Splicing

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

Other links and lift over

dbSNP: rs3759501; hg19: chr13-103720678;