rs9317708

Variant names:

• chr13-68576784-G-A
• rs9317708

Your query was ambiguous. Multiple possible variants found:

• chr13-68576784-G-A
• chr13-68576784-G-C

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 0.558 in 151,792 control chromosomes in the GnomAD database, including 24,164 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 0.56 (24164 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0350
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.609 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: 0.558 AC: 84635 AN: 151674 Hom.: 24156 Cov.: 31

Gnomad AFR AF: 0.444

Gnomad AMI AF: 0.644

Gnomad AMR AF: 0.610

Gnomad ASJ AF: 0.562

Gnomad EAS AF: 0.582

Gnomad SAS AF: 0.550

Gnomad FIN AF: 0.550

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.614

Gnomad OTH AF: 0.572

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

GnomAD4 genome AF: 0.558 AC: 84666 AN: 151792 Hom.: 24164 Cov.: 31 AF XY: 0.552 AC XY: 40963 AN XY: 74174

African (AFR) AF: 0.443 AC: 18362 AN: 41404

American (AMR) AF: 0.610 AC: 9299 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.562 AC: 1947 AN: 3466

East Asian (EAS) AF: 0.581 AC: 2990 AN: 5142

South Asian (SAS) AF: 0.550 AC: 2653 AN: 4822

European-Finnish (FIN) AF: 0.550 AC: 5794 AN: 10540

Middle Eastern (MID) AF: 0.592 AC: 174 AN: 294

European-Non Finnish (NFE) AF: 0.614 AC: 41655 AN: 67870

Other (OTH) AF: 0.572 AC: 1205 AN: 2106

Alfa AF: 0.582 Hom.: 3381

Bravo AF: 0.558

Asia WGS AF: 0.540 AC: 1875 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.3
DANN	Benign	0.33
PhyloP100		-0.035

Splicing

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

Other links and lift over

dbSNP: rs9317708; hg19: chr13-69150916;