rs10118617

Variant names:

• chr9-96788187-T-C
• rs10118617

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 0.143 in 152,164 control chromosomes in the GnomAD database, including 3,547 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 0.14 (3547 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.964
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.381 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.143 AC: 21698 AN: 152046 Hom.: 3514 Cov.: 32

Gnomad AFR AF: 0.385

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.0686

Gnomad ASJ AF: 0.0245

Gnomad EAS AF: 0.340

Gnomad SAS AF: 0.115

Gnomad FIN AF: 0.0926

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0165

Gnomad OTH AF: 0.0980

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

GnomAD4 genome AF: 0.143 AC: 21770 AN: 152164 Hom.: 3547 Cov.: 32 AF XY: 0.147 AC XY: 10904 AN XY: 74398

African (AFR) AF: 0.386 AC: 16004 AN: 41474

American (AMR) AF: 0.0684 AC: 1045 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0245 AC: 85 AN: 3472

East Asian (EAS) AF: 0.339 AC: 1748 AN: 5152

South Asian (SAS) AF: 0.114 AC: 548 AN: 4816

European-Finnish (FIN) AF: 0.0926 AC: 982 AN: 10610

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0165 AC: 1120 AN: 68034

Other (OTH) AF: 0.0970 AC: 205 AN: 2114

Alfa AF: 0.0947 Hom.: 393

Bravo AF: 0.153

Asia WGS AF: 0.195 AC: 676 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.4
DANN	Benign	0.68
PhyloP100		-0.96

Splicing

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

Other links and lift over

dbSNP: rs10118617; hg19: chr9-99550469;