rs9317390

Variant names:

• chr13-64153397-A-G
• rs9317390

Your query was ambiguous. Multiple possible variants found:

• chr13-64153397-A-G
• chr13-64153397-A-T

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 0.374 in 151,816 control chromosomes in the GnomAD database, including 12,477 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 0.37 (12477 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.190
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.58 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: 0.374 AC: 56776 AN: 151698 Hom.: 12471 Cov.: 31

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.334

Gnomad AMR AF: 0.452

Gnomad ASJ AF: 0.420

Gnomad EAS AF: 0.597

Gnomad SAS AF: 0.428

Gnomad FIN AF: 0.499

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.462

Gnomad OTH AF: 0.370

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

GnomAD4 genome AF: 0.374 AC: 56793 AN: 151816 Hom.: 12477 Cov.: 31 AF XY: 0.379 AC XY: 28079 AN XY: 74164

African (AFR) AF: 0.134 AC: 5540 AN: 41474

American (AMR) AF: 0.453 AC: 6882 AN: 15202

Ashkenazi Jewish (ASJ) AF: 0.420 AC: 1455 AN: 3464

East Asian (EAS) AF: 0.597 AC: 3071 AN: 5142

South Asian (SAS) AF: 0.429 AC: 2067 AN: 4814

European-Finnish (FIN) AF: 0.499 AC: 5254 AN: 10532

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.462 AC: 31344 AN: 67882

Other (OTH) AF: 0.369 AC: 775 AN: 2102

Alfa AF: 0.409 Hom.: 2415

Bravo AF: 0.362

Asia WGS AF: 0.473 AC: 1644 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.65
DANN	Benign	0.50
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs9317390; hg19: chr13-64727530;