rs10979500

Variant names:

• chr9-108799186-G-A
• rs10979500

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 0.0913 in 152,108 control chromosomes in the GnomAD database, including 852 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 0.091 (852 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.336

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.118 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: 0.0914 AC: 13888 AN: 151990 Hom.: 853 Cov.: 32

Gnomad AFR AF: 0.0234

Gnomad AMI AF: 0.113

Gnomad AMR AF: 0.0755

Gnomad ASJ AF: 0.0980

Gnomad EAS AF: 0.115

Gnomad SAS AF: 0.0946

Gnomad FIN AF: 0.181

Gnomad MID AF: 0.0510

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.0923

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

GnomAD4 genome AF: 0.0913 AC: 13882 AN: 152108 Hom.: 852 Cov.: 32 AF XY: 0.0951 AC XY: 7067 AN XY: 74350

Gnomad4 AFR AF: 0.0234

Gnomad4 AMR AF: 0.0754

Gnomad4 ASJ AF: 0.0980

Gnomad4 EAS AF: 0.115

Gnomad4 SAS AF: 0.0939

Gnomad4 FIN AF: 0.181

Gnomad4 NFE AF: 0.120

Gnomad4 OTH AF: 0.0919

Alfa AF: 0.103 Hom.: 147

Bravo AF: 0.0806

Asia WGS AF: 0.130 AC: 450 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.8
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10979500; hg19: chr9-111561466;