rs10813887

chr9-32879343-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 0.747 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.748 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

Gnomad4 AFR AF: 0.488

Gnomad4 AMR AF: 0.839

Gnomad4 ASJ AF: 0.746

Gnomad4 EAS AF: 0.814

Gnomad4 SAS AF: 0.800

Gnomad4 FIN AF: 0.861

Gnomad4 NFE AF: 0.857

Gnomad4 OTH AF: 0.769

Alfa AF: 0.837 Hom.: 105160

Bravo AF: 0.736

Asia WGS AF: 0.788 AC: 2741 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	0.80
Dann	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

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