rs9315242

Variant names:

• chr13-33722889-T-C
• rs9315242

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 0.0773 in 152,236 control chromosomes in the GnomAD database, including 997 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 0.077 (997 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.250

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.24 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: 0.0771 AC: 11734 AN: 152118 Hom.: 993 Cov.: 32

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0727

Gnomad ASJ AF: 0.0110

Gnomad EAS AF: 0.252

Gnomad SAS AF: 0.0494

Gnomad FIN AF: 0.0230

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0110

Gnomad OTH AF: 0.0640

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

GnomAD4 genome AF: 0.0773 AC: 11772 AN: 152236 Hom.: 997 Cov.: 32 AF XY: 0.0786 AC XY: 5850 AN XY: 74446

Gnomad4 AFR AF: 0.191

Gnomad4 AMR AF: 0.0730

Gnomad4 ASJ AF: 0.0110

Gnomad4 EAS AF: 0.252

Gnomad4 SAS AF: 0.0491

Gnomad4 FIN AF: 0.0230

Gnomad4 NFE AF: 0.0110

Gnomad4 OTH AF: 0.0633

Alfa AF: 0.0455 Hom.: 65

Bravo AF: 0.0881

Asia WGS AF: 0.174 AC: 603 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.1
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9315242; hg19: chr13-34297026;