rs9317708

Positions:

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

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.443

Gnomad4 AMR AF: 0.610

Gnomad4 ASJ AF: 0.562

Gnomad4 EAS AF: 0.581

Gnomad4 SAS AF: 0.550

Gnomad4 FIN AF: 0.550

Gnomad4 NFE AF: 0.614

Gnomad4 OTH AF: 0.572

Alfa AF: 0.589 Hom.: 3316

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9317708; hg19: chr13-69150916;