rs9510171

chr13-22385991-G-A

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 0.675 in 152,166 control chromosomes in the GnomAD database, including 40,805 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 0.67 (40805 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.876 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: 0.675 AC: 102645 AN: 152048 Hom.: 40804 Cov.: 33

Gnomad AFR AF: 0.223

Gnomad AMI AF: 0.962

Gnomad AMR AF: 0.729

Gnomad ASJ AF: 0.874

Gnomad EAS AF: 0.708

Gnomad SAS AF: 0.836

Gnomad FIN AF: 0.839

Gnomad MID AF: 0.823

Gnomad NFE AF: 0.882

Gnomad OTH AF: 0.721

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

GnomAD4 genome AF: 0.675 AC: 102651 AN: 152166 Hom.: 40805 Cov.: 33 AF XY: 0.677 AC XY: 50308 AN XY: 74356

Gnomad4 AFR AF: 0.222

Gnomad4 AMR AF: 0.729

Gnomad4 ASJ AF: 0.874

Gnomad4 EAS AF: 0.709

Gnomad4 SAS AF: 0.837

Gnomad4 FIN AF: 0.839

Gnomad4 NFE AF: 0.882

Gnomad4 OTH AF: 0.721

Alfa AF: 0.845 Hom.: 74916

Bravo AF: 0.641

Asia WGS AF: 0.737 AC: 2564 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	2.4
Dann	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9510171; hg19: chr13-22960130;