13-103439195-C-T

Variant names:

• chr13-103439195-C-T
• rs583464

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 0.678 in 151,928 control chromosomes in the GnomAD database, including 35,569 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 0.68 (35569 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.758
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.757 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: 0.679 AC: 103013 AN: 151810 Hom.: 35548 Cov.: 32

Gnomad AFR AF: 0.545

Gnomad AMI AF: 0.618

Gnomad AMR AF: 0.769

Gnomad ASJ AF: 0.673

Gnomad EAS AF: 0.652

Gnomad SAS AF: 0.616

Gnomad FIN AF: 0.702

Gnomad MID AF: 0.745

Gnomad NFE AF: 0.743

Gnomad OTH AF: 0.692

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

GnomAD4 genome AF: 0.678 AC: 103071 AN: 151928 Hom.: 35569 Cov.: 32 AF XY: 0.676 AC XY: 50199 AN XY: 74256

African (AFR) AF: 0.545 AC: 22569 AN: 41398

American (AMR) AF: 0.769 AC: 11744 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.673 AC: 2338 AN: 3472

East Asian (EAS) AF: 0.652 AC: 3373 AN: 5170

South Asian (SAS) AF: 0.614 AC: 2963 AN: 4822

European-Finnish (FIN) AF: 0.702 AC: 7397 AN: 10540

Middle Eastern (MID) AF: 0.757 AC: 221 AN: 292

European-Non Finnish (NFE) AF: 0.743 AC: 50456 AN: 67948

Other (OTH) AF: 0.688 AC: 1448 AN: 2104

Alfa AF: 0.618 Hom.: 1867

Bravo AF: 0.679

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.55
DANN	Benign	0.69
PhyloP100		-0.76

Splicing

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

Other links and lift over

dbSNP: rs583464; hg19: chr13-104091545;