13-103317141-G-A

Variant names:

• chr13-103317141-G-A
• rs4771450

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 0.652 in 151,992 control chromosomes in the GnomAD database, including 32,561 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 0.65 (32561 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.852
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.714 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.652 AC: 98968 AN: 151872 Hom.: 32537 Cov.: 32

Gnomad AFR AF: 0.721

Gnomad AMI AF: 0.424

Gnomad AMR AF: 0.630

Gnomad ASJ AF: 0.660

Gnomad EAS AF: 0.405

Gnomad SAS AF: 0.686

Gnomad FIN AF: 0.611

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.640

Gnomad OTH AF: 0.647

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

GnomAD4 genome AF: 0.652 AC: 99045 AN: 151992 Hom.: 32561 Cov.: 32 AF XY: 0.647 AC XY: 48060 AN XY: 74266

African (AFR) AF: 0.721 AC: 29904 AN: 41478

American (AMR) AF: 0.630 AC: 9617 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.660 AC: 2290 AN: 3470

East Asian (EAS) AF: 0.406 AC: 2097 AN: 5164

South Asian (SAS) AF: 0.687 AC: 3311 AN: 4822

European-Finnish (FIN) AF: 0.611 AC: 6434 AN: 10534

Middle Eastern (MID) AF: 0.619 AC: 182 AN: 294

European-Non Finnish (NFE) AF: 0.640 AC: 43460 AN: 67942

Other (OTH) AF: 0.647 AC: 1363 AN: 2108

Alfa AF: 0.646 Hom.: 23462

Bravo AF: 0.656

Asia WGS AF: 0.606 AC: 2108 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.9
DANN	Benign	0.72
PhyloP100		0.85

Splicing

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

Other links and lift over

dbSNP: rs4771450; hg19: chr13-103969491;