rs9509124

Variant names:

• chr13-20267631-G-A
• rs9509124

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.160 AC: 6625 AN: 41444

American (AMR) AF: 0.392 AC: 5986 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.371 AC: 1286 AN: 3468

East Asian (EAS) AF: 0.519 AC: 2679 AN: 5160

South Asian (SAS) AF: 0.387 AC: 1864 AN: 4822

European-Finnish (FIN) AF: 0.350 AC: 3670 AN: 10496

Middle Eastern (MID) AF: 0.527 AC: 155 AN: 294

European-Non Finnish (NFE) AF: 0.400 AC: 27208 AN: 67962

Other (OTH) AF: 0.366 AC: 771 AN: 2108

Alfa AF: 0.384 Hom.: 46746

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
PhyloP100		-0.059

Splicing

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

Other links and lift over

dbSNP: rs9509124; hg19: chr13-20841770;