rs9509124

chr13-20267631-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 0.333 in 151,932 control chromosomes in the GnomAD database, including 9,355 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 0.33 (9355 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0590

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.503 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: 0.333 AC: 50604 AN: 151816 Hom.: 9359 Cov.: 32

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.399

Gnomad AMR AF: 0.392

Gnomad ASJ AF: 0.371

Gnomad EAS AF: 0.519

Gnomad SAS AF: 0.388

Gnomad FIN AF: 0.350

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.400

Gnomad OTH AF: 0.364

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

GnomAD4 genome AF: 0.333 AC: 50607 AN: 151932 Hom.: 9355 Cov.: 32 AF XY: 0.331 AC XY: 24589 AN XY: 74224

Gnomad4 AFR AF: 0.160

Gnomad4 AMR AF: 0.392

Gnomad4 ASJ AF: 0.371

Gnomad4 EAS AF: 0.519

Gnomad4 SAS AF: 0.387

Gnomad4 FIN AF: 0.350

Gnomad4 NFE AF: 0.400

Gnomad4 OTH AF: 0.366

Alfa AF: 0.400 Hom.: 22992

Bravo AF: 0.331

Asia WGS AF: 0.380 AC: 1323 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.83
Dann	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9509124; hg19: chr13-20841770;