rs9318892

Variant names:

• chr13-82645272-G-A
• rs9318892

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 0.389 in 151,864 control chromosomes in the GnomAD database, including 11,847 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 0.39 (11847 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0590
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.467 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: 0.389 AC: 59045 AN: 151746 Hom.: 11847 Cov.: 31

Gnomad AFR AF: 0.309

Gnomad AMI AF: 0.440

Gnomad AMR AF: 0.476

Gnomad ASJ AF: 0.501

Gnomad EAS AF: 0.298

Gnomad SAS AF: 0.473

Gnomad FIN AF: 0.307

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.424

Gnomad OTH AF: 0.418

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

GnomAD4 genome AF: 0.389 AC: 59050 AN: 151864 Hom.: 11847 Cov.: 31 AF XY: 0.388 AC XY: 28790 AN XY: 74188

African (AFR) AF: 0.308 AC: 12776 AN: 41422

American (AMR) AF: 0.476 AC: 7266 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.501 AC: 1738 AN: 3466

East Asian (EAS) AF: 0.297 AC: 1528 AN: 5152

South Asian (SAS) AF: 0.472 AC: 2277 AN: 4822

European-Finnish (FIN) AF: 0.307 AC: 3230 AN: 10518

Middle Eastern (MID) AF: 0.565 AC: 166 AN: 294

European-Non Finnish (NFE) AF: 0.424 AC: 28802 AN: 67932

Other (OTH) AF: 0.414 AC: 866 AN: 2094

Alfa AF: 0.426 Hom.: 7259

Bravo AF: 0.398

Asia WGS AF: 0.370 AC: 1285 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.8
DANN	Benign	0.43
PhyloP100		0.059

Splicing

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

Other links and lift over

dbSNP: rs9318892; hg19: chr13-83219407;