9-97875057-C-T

Variant names:

• chr9-97875057-C-T
• rs10119795

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 0.502 in 152,016 control chromosomes in the GnomAD database, including 20,205 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 0.50 (20205 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.225
• Publications: 17 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.53).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.81 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: 0.502 AC: 76202 AN: 151898 Hom.: 20172 Cov.: 32

Gnomad AFR AF: 0.631

Gnomad AMI AF: 0.347

Gnomad AMR AF: 0.492

Gnomad ASJ AF: 0.396

Gnomad EAS AF: 0.831

Gnomad SAS AF: 0.576

Gnomad FIN AF: 0.492

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.405

Gnomad OTH AF: 0.471

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

GnomAD4 genome AF: 0.502 AC: 76272 AN: 152016 Hom.: 20205 Cov.: 32 AF XY: 0.509 AC XY: 37845 AN XY: 74332

African (AFR) AF: 0.631 AC: 26173 AN: 41508

American (AMR) AF: 0.492 AC: 7525 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.396 AC: 1375 AN: 3472

East Asian (EAS) AF: 0.831 AC: 4247 AN: 5110

South Asian (SAS) AF: 0.574 AC: 2771 AN: 4824

European-Finnish (FIN) AF: 0.492 AC: 5202 AN: 10576

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.405 AC: 27522 AN: 67924

Other (OTH) AF: 0.473 AC: 999 AN: 2112

Alfa AF: 0.443 Hom.: 40790

Bravo AF: 0.507

Asia WGS AF: 0.654 AC: 2275 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.53
CADD	Benign	4.9
DANN	Benign	0.56
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs10119795; hg19: chr9-100637339;