rs9315053

Variant names:

• chr13-30764963-T-G
• rs9315053

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 0.244 in 152,232 control chromosomes in the GnomAD database, including 5,727 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 0.24 (5727 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0130

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.322 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: 0.244 AC: 37111 AN: 152114 Hom.: 5726 Cov.: 33

Gnomad AFR AF: 0.0582

Gnomad AMI AF: 0.308

Gnomad AMR AF: 0.329

Gnomad ASJ AF: 0.250

Gnomad EAS AF: 0.252

Gnomad SAS AF: 0.246

Gnomad FIN AF: 0.341

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.321

Gnomad OTH AF: 0.242

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

GnomAD4 genome AF: 0.244 AC: 37119 AN: 152232 Hom.: 5727 Cov.: 33 AF XY: 0.246 AC XY: 18321 AN XY: 74408

Gnomad4 AFR AF: 0.0581

Gnomad4 AMR AF: 0.330

Gnomad4 ASJ AF: 0.250

Gnomad4 EAS AF: 0.252

Gnomad4 SAS AF: 0.247

Gnomad4 FIN AF: 0.341

Gnomad4 NFE AF: 0.321

Gnomad4 OTH AF: 0.240

Alfa AF: 0.274 Hom.: 944

Bravo AF: 0.237

Asia WGS AF: 0.206 AC: 714 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.0
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9315053; hg19: chr13-31339100;