rs10979500

Variant names:

• chr9-108799186-G-A
• rs10979500

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 0.0913 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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0234 AC: 972 AN: 41518

American (AMR) AF: 0.0754 AC: 1152 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0980 AC: 340 AN: 3468

East Asian (EAS) AF: 0.115 AC: 592 AN: 5160

South Asian (SAS) AF: 0.0939 AC: 452 AN: 4814

European-Finnish (FIN) AF: 0.181 AC: 1910 AN: 10560

Middle Eastern (MID) AF: 0.0548 AC: 16 AN: 292

European-Non Finnish (NFE) AF: 0.120 AC: 8151 AN: 67984

Other (OTH) AF: 0.0919 AC: 194 AN: 2112

Alfa AF: 0.100 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
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs10979500; hg19: chr9-111561466;