rs9317975

Variant names:

• chr13-70932106-G-A
• rs9317975

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 0.347 in 151,708 control chromosomes in the GnomAD database, including 9,456 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 0.35 (9456 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.17

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.61).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.4 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: 0.347 AC: 52593 AN: 151588 Hom.: 9444 Cov.: 32

Gnomad AFR AF: 0.262

Gnomad AMI AF: 0.157

Gnomad AMR AF: 0.407

Gnomad ASJ AF: 0.421

Gnomad EAS AF: 0.292

Gnomad SAS AF: 0.336

Gnomad FIN AF: 0.463

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.371

Gnomad OTH AF: 0.350

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

GnomAD4 genome AF: 0.347 AC: 52632 AN: 151708 Hom.: 9456 Cov.: 32 AF XY: 0.350 AC XY: 25969 AN XY: 74106

Gnomad4 AFR AF: 0.262

Gnomad4 AMR AF: 0.408

Gnomad4 ASJ AF: 0.421

Gnomad4 EAS AF: 0.292

Gnomad4 SAS AF: 0.335

Gnomad4 FIN AF: 0.463

Gnomad4 NFE AF: 0.371

Gnomad4 OTH AF: 0.350

Alfa AF: 0.370 Hom.: 1297

Bravo AF: 0.340

Asia WGS AF: 0.283 AC: 983 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	8.3
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9317975; hg19: chr13-71506238;