rs9567731

Variant names:

• chr13-46826551-A-G
• rs9567731

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 0.77 in 152,188 control chromosomes in the GnomAD database, including 45,805 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 0.77 (45805 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.369

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.892 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: 0.770 AC: 117113 AN: 152070 Hom.: 45775 Cov.: 33

Gnomad AFR AF: 0.900

Gnomad AMI AF: 0.693

Gnomad AMR AF: 0.745

Gnomad ASJ AF: 0.798

Gnomad EAS AF: 0.733

Gnomad SAS AF: 0.590

Gnomad FIN AF: 0.633

Gnomad MID AF: 0.717

Gnomad NFE AF: 0.733

Gnomad OTH AF: 0.778

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

GnomAD4 genome AF: 0.770 AC: 117195 AN: 152188 Hom.: 45805 Cov.: 33 AF XY: 0.762 AC XY: 56681 AN XY: 74382

Gnomad4 AFR AF: 0.900

Gnomad4 AMR AF: 0.745

Gnomad4 ASJ AF: 0.798

Gnomad4 EAS AF: 0.733

Gnomad4 SAS AF: 0.588

Gnomad4 FIN AF: 0.633

Gnomad4 NFE AF: 0.733

Gnomad4 OTH AF: 0.774

Alfa AF: 0.745 Hom.: 41704

Bravo AF: 0.791

Asia WGS AF: 0.666 AC: 2319 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.2
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9567731; hg19: chr13-47400686;