rs9509167

Variant names:

• chr13-20333362-G-T
• rs9509167

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 0.448 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.205 AC: 8505 AN: 41434

American (AMR) AF: 0.547 AC: 8363 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.373 AC: 1292 AN: 3464

East Asian (EAS) AF: 0.268 AC: 1382 AN: 5166

South Asian (SAS) AF: 0.515 AC: 2480 AN: 4814

European-Finnish (FIN) AF: 0.552 AC: 5830 AN: 10560

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.569 AC: 38644 AN: 67970

Other (OTH) AF: 0.452 AC: 952 AN: 2108

Alfa AF: 0.533 Hom.: 13129

Bravo AF: 0.435

Asia WGS AF: 0.458 AC: 1592 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.9
DANN	Benign	0.78
PhyloP100		0.55

Splicing

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

Other links and lift over

dbSNP: rs9509167; hg19: chr13-20907501;