9-80980146-G-A

Variant names:

• chr9-80980146-G-A
• rs13285452

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 0.566 in 151,956 control chromosomes in the GnomAD database, including 25,762 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 0.57 (25762 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.943
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.756 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.566 AC: 85866 AN: 151838 Hom.: 25736 Cov.: 33

Gnomad AFR AF: 0.763

Gnomad AMI AF: 0.312

Gnomad AMR AF: 0.581

Gnomad ASJ AF: 0.558

Gnomad EAS AF: 0.712

Gnomad SAS AF: 0.645

Gnomad FIN AF: 0.420

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.451

Gnomad OTH AF: 0.577

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

GnomAD4 genome AF: 0.566 AC: 85952 AN: 151956 Hom.: 25762 Cov.: 33 AF XY: 0.568 AC XY: 42152 AN XY: 74232

African (AFR) AF: 0.763 AC: 31658 AN: 41482

American (AMR) AF: 0.581 AC: 8862 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.558 AC: 1937 AN: 3470

East Asian (EAS) AF: 0.711 AC: 3671 AN: 5162

South Asian (SAS) AF: 0.644 AC: 3103 AN: 4822

European-Finnish (FIN) AF: 0.420 AC: 4419 AN: 10528

Middle Eastern (MID) AF: 0.554 AC: 163 AN: 294

European-Non Finnish (NFE) AF: 0.451 AC: 30643 AN: 67920

Other (OTH) AF: 0.575 AC: 1212 AN: 2108

Alfa AF: 0.502 Hom.: 4706

Bravo AF: 0.583

Asia WGS AF: 0.686 AC: 2381 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.53
DANN	Benign	0.29
PhyloP100		-0.94

Splicing

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

Other links and lift over

dbSNP: rs13285452; hg19: chr9-83595061;