rs9531267

chr13-81930550-C-T

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 0.557 in 151,186 control chromosomes in the GnomAD database, including 23,721 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 (23721 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.173

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.624 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.557 AC: 84226 AN: 151080 Hom.: 23700 Cov.: 31

Gnomad AFR AF: 0.631

Gnomad AMI AF: 0.586

Gnomad AMR AF: 0.500

Gnomad ASJ AF: 0.453

Gnomad EAS AF: 0.629

Gnomad SAS AF: 0.639

Gnomad FIN AF: 0.564

Gnomad MID AF: 0.580

Gnomad NFE AF: 0.519

Gnomad OTH AF: 0.552

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

GnomAD4 genome AF: 0.557 AC: 84282 AN: 151186 Hom.: 23721 Cov.: 31 AF XY: 0.561 AC XY: 41429 AN XY: 73876

Gnomad4 AFR AF: 0.630

Gnomad4 AMR AF: 0.500

Gnomad4 ASJ AF: 0.453

Gnomad4 EAS AF: 0.628

Gnomad4 SAS AF: 0.638

Gnomad4 FIN AF: 0.564

Gnomad4 NFE AF: 0.519

Gnomad4 OTH AF: 0.554

Alfa AF: 0.530 Hom.: 9877

Bravo AF: 0.554

Asia WGS AF: 0.638 AC: 2166 AN: 3398

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.99
Dann	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9531267; hg19: chr13-82504685;