chr13-73349748-G-A

Variant names:

• chr13-73349748-G-A
• rs9318166

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 0.259 in 151,898 control chromosomes in the GnomAD database, including 5,457 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 0.26 (5457 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.590
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.338 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: 0.259 AC: 39330 AN: 151778 Hom.: 5449 Cov.: 32

Gnomad AFR AF: 0.343

Gnomad AMI AF: 0.152

Gnomad AMR AF: 0.262

Gnomad ASJ AF: 0.281

Gnomad EAS AF: 0.292

Gnomad SAS AF: 0.237

Gnomad FIN AF: 0.245

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.258

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

GnomAD4 genome AF: 0.259 AC: 39362 AN: 151898 Hom.: 5457 Cov.: 32 AF XY: 0.260 AC XY: 19333 AN XY: 74238

African (AFR) AF: 0.342 AC: 14194 AN: 41446

American (AMR) AF: 0.262 AC: 3995 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.281 AC: 975 AN: 3468

East Asian (EAS) AF: 0.292 AC: 1505 AN: 5154

South Asian (SAS) AF: 0.237 AC: 1141 AN: 4812

European-Finnish (FIN) AF: 0.245 AC: 2588 AN: 10556

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.209 AC: 14220 AN: 67882

Other (OTH) AF: 0.255 AC: 535 AN: 2102

Alfa AF: 0.231 Hom.: 11524

Bravo AF: 0.266

Asia WGS AF: 0.236 AC: 819 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.6
DANN	Benign	0.22
PhyloP100		0.59

Splicing

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

Other links and lift over

dbSNP: rs9318166; hg19: chr13-73923885; COSMIC: COSV69363903;