rs9509167

chr13-20333362-G-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 0.448 in 152,006 control chromosomes in the GnomAD database, including 17,405 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 0.45 (17405 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.554

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.564 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: 0.448 AC: 68092 AN: 151890 Hom.: 17400 Cov.: 32

Gnomad AFR AF: 0.205

Gnomad AMI AF: 0.624

Gnomad AMR AF: 0.547

Gnomad ASJ AF: 0.373

Gnomad EAS AF: 0.268

Gnomad SAS AF: 0.513

Gnomad FIN AF: 0.552

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.569

Gnomad OTH AF: 0.449

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

GnomAD4 genome AF: 0.448 AC: 68132 AN: 152006 Hom.: 17405 Cov.: 32 AF XY: 0.447 AC XY: 33188 AN XY: 74308

Gnomad4 AFR AF: 0.205

Gnomad4 AMR AF: 0.547

Gnomad4 ASJ AF: 0.373

Gnomad4 EAS AF: 0.268

Gnomad4 SAS AF: 0.515

Gnomad4 FIN AF: 0.552

Gnomad4 NFE AF: 0.569

Gnomad4 OTH AF: 0.452

Alfa AF: 0.535 Hom.: 11950

Bravo AF: 0.435

Asia WGS AF: 0.458 AC: 1592 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	2.9
Dann	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9509167; hg19: chr13-20907501;