13-104305373-C-T

Variant names:

• chr13-104305373-C-T
• rs728555

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 0.579 in 151,968 control chromosomes in the GnomAD database, including 25,967 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 0.58 (25967 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.56
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.08).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.624 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: 0.579 AC: 87854 AN: 151848 Hom.: 25947 Cov.: 32

Gnomad AFR AF: 0.539

Gnomad AMI AF: 0.741

Gnomad AMR AF: 0.634

Gnomad ASJ AF: 0.755

Gnomad EAS AF: 0.279

Gnomad SAS AF: 0.441

Gnomad FIN AF: 0.522

Gnomad MID AF: 0.764

Gnomad NFE AF: 0.618

Gnomad OTH AF: 0.628

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

GnomAD4 genome AF: 0.579 AC: 87925 AN: 151968 Hom.: 25967 Cov.: 32 AF XY: 0.572 AC XY: 42503 AN XY: 74302

African (AFR) AF: 0.540 AC: 22349 AN: 41416

American (AMR) AF: 0.634 AC: 9693 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.755 AC: 2620 AN: 3470

East Asian (EAS) AF: 0.279 AC: 1440 AN: 5168

South Asian (SAS) AF: 0.441 AC: 2126 AN: 4822

European-Finnish (FIN) AF: 0.522 AC: 5511 AN: 10556

Middle Eastern (MID) AF: 0.779 AC: 229 AN: 294

European-Non Finnish (NFE) AF: 0.618 AC: 41967 AN: 67934

Other (OTH) AF: 0.622 AC: 1314 AN: 2112

Alfa AF: 0.590 Hom.: 3481

Bravo AF: 0.586

Asia WGS AF: 0.403 AC: 1400 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.010
DANN	Benign	0.41
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs728555; hg19: chr13-104957723; COSMIC: COSV107153122;