13-73342491-C-T

Variant names:

• chr13-73342491-C-T
• rs9543325

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 0.485 in 152,026 control chromosomes in the GnomAD database, including 21,654 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 0.49 (21654 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.185
• Publications: 73 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.631 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: 0.486 AC: 73804 AN: 151908 Hom.: 21657 Cov.: 31

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.499

Gnomad AMR AF: 0.582

Gnomad ASJ AF: 0.517

Gnomad EAS AF: 0.566

Gnomad SAS AF: 0.637

Gnomad FIN AF: 0.642

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.636

Gnomad OTH AF: 0.482

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

GnomAD4 genome AF: 0.485 AC: 73799 AN: 152026 Hom.: 21654 Cov.: 31 AF XY: 0.489 AC XY: 36349 AN XY: 74298

African (AFR) AF: 0.134 AC: 5562 AN: 41494

American (AMR) AF: 0.583 AC: 8901 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.517 AC: 1792 AN: 3468

East Asian (EAS) AF: 0.566 AC: 2913 AN: 5148

South Asian (SAS) AF: 0.636 AC: 3055 AN: 4806

European-Finnish (FIN) AF: 0.642 AC: 6796 AN: 10578

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.636 AC: 43183 AN: 67938

Other (OTH) AF: 0.482 AC: 1019 AN: 2114

Alfa AF: 0.586 Hom.: 124929

Bravo AF: 0.465

Asia WGS AF: 0.567 AC: 1973 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.9
DANN	Benign	0.58
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs9543325; hg19: chr13-73916628;