rs9567731

chr13-46826551-A-G

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;