rs10813887

Variant names:

• chr9-32879343-G-A
• rs10813887

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;