rs9315632

Variant names:

• chr13-38942490-G-T
• rs9315632

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 0.252 in 152,062 control chromosomes in the GnomAD database, including 5,577 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 0.25 (5577 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.840

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.384 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: 0.252 AC: 38315 AN: 151942 Hom.: 5551 Cov.: 32

Gnomad AFR AF: 0.389

Gnomad AMI AF: 0.247

Gnomad AMR AF: 0.272

Gnomad ASJ AF: 0.222

Gnomad EAS AF: 0.235

Gnomad SAS AF: 0.280

Gnomad FIN AF: 0.142

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.184

Gnomad OTH AF: 0.238

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

GnomAD4 genome AF: 0.252 AC: 38393 AN: 152062 Hom.: 5577 Cov.: 32 AF XY: 0.252 AC XY: 18696 AN XY: 74328

Gnomad4 AFR AF: 0.389

Gnomad4 AMR AF: 0.273

Gnomad4 ASJ AF: 0.222

Gnomad4 EAS AF: 0.235

Gnomad4 SAS AF: 0.280

Gnomad4 FIN AF: 0.142

Gnomad4 NFE AF: 0.184

Gnomad4 OTH AF: 0.236

Alfa AF: 0.199 Hom.: 6940

Bravo AF: 0.270

Asia WGS AF: 0.279 AC: 972 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.79
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9315632; hg19: chr13-39516627;