9-32879343-G-A

Variant names:

• chr9-32879343-G-A
• rs10813887

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 0.747 in 151,722 control chromosomes in the GnomAD database, including 44,421 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 0.75 (44421 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.851 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: 0.748 AC: 113340 AN: 151604 Hom.: 44394 Cov.: 29

Gnomad AFR AF: 0.488

Gnomad AMI AF: 0.792

Gnomad AMR AF: 0.839

Gnomad ASJ AF: 0.746

Gnomad EAS AF: 0.814

Gnomad SAS AF: 0.798

Gnomad FIN AF: 0.861

Gnomad MID AF: 0.694

Gnomad NFE AF: 0.857

Gnomad OTH AF: 0.772

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

GnomAD4 genome AF: 0.747 AC: 113410 AN: 151722 Hom.: 44421 Cov.: 29 AF XY: 0.748 AC XY: 55497 AN XY: 74158

African (AFR) AF: 0.488 AC: 20150 AN: 41270

American (AMR) AF: 0.839 AC: 12805 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.746 AC: 2590 AN: 3470

East Asian (EAS) AF: 0.814 AC: 4217 AN: 5180

South Asian (SAS) AF: 0.800 AC: 3830 AN: 4788

European-Finnish (FIN) AF: 0.861 AC: 9058 AN: 10520

Middle Eastern (MID) AF: 0.685 AC: 200 AN: 292

European-Non Finnish (NFE) AF: 0.857 AC: 58220 AN: 67926

Other (OTH) AF: 0.769 AC: 1619 AN: 2104

Alfa AF: 0.817 Hom.: 161060

Bravo AF: 0.736

Asia WGS AF: 0.788 AC: 2741 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.80
DANN	Benign	0.76
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs10813887; hg19: chr9-32879341; COSMIC: COSV60352013;