rs10119760

Variant names:

• chr9-97862320-G-C
• rs10119760

Your query was ambiguous. Multiple possible variants found:

• chr9-97862320-G-C
• chr9-97862320-G-T

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 0.719 in 152,088 control chromosomes in the GnomAD database, including 40,363 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 0.72 (40363 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.966
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.9 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: 0.718 AC: 109185 AN: 151970 Hom.: 40308 Cov.: 32

Gnomad AFR AF: 0.887

Gnomad AMI AF: 0.426

Gnomad AMR AF: 0.691

Gnomad ASJ AF: 0.636

Gnomad EAS AF: 0.921

Gnomad SAS AF: 0.676

Gnomad FIN AF: 0.647

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.629

Gnomad OTH AF: 0.711

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

GnomAD4 genome AF: 0.719 AC: 109290 AN: 152088 Hom.: 40363 Cov.: 32 AF XY: 0.721 AC XY: 53577 AN XY: 74354

African (AFR) AF: 0.887 AC: 36846 AN: 41530

American (AMR) AF: 0.692 AC: 10565 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.636 AC: 2209 AN: 3472

East Asian (EAS) AF: 0.921 AC: 4762 AN: 5168

South Asian (SAS) AF: 0.675 AC: 3246 AN: 4812

European-Finnish (FIN) AF: 0.647 AC: 6834 AN: 10564

Middle Eastern (MID) AF: 0.707 AC: 208 AN: 294

European-Non Finnish (NFE) AF: 0.629 AC: 42732 AN: 67958

Other (OTH) AF: 0.710 AC: 1500 AN: 2112

Alfa AF: 0.574 Hom.: 1754

Bravo AF: 0.731

Asia WGS AF: 0.785 AC: 2733 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	0.57
DANN	Benign	0.85
PhyloP100		-0.97

Splicing

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

Other links and lift over

dbSNP: rs10119760; hg19: chr9-100624602;