rs9531267

Variant names:

• chr13-81930550-C-T
• rs9531267

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.630 AC: 26023 AN: 41284

American (AMR) AF: 0.500 AC: 7580 AN: 15152

Ashkenazi Jewish (ASJ) AF: 0.453 AC: 1566 AN: 3460

East Asian (EAS) AF: 0.628 AC: 3230 AN: 5140

South Asian (SAS) AF: 0.638 AC: 3062 AN: 4798

European-Finnish (FIN) AF: 0.564 AC: 5858 AN: 10394

Middle Eastern (MID) AF: 0.571 AC: 153 AN: 268

European-Non Finnish (NFE) AF: 0.519 AC: 35120 AN: 67690

Other (OTH) AF: 0.554 AC: 1158 AN: 2092

Alfa AF: 0.528 Hom.: 10880

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
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs9531267; hg19: chr13-82504685;