rs960312

Variant names:

• chr9-117681501-G-A
• rs960312

Your query was ambiguous. Multiple possible variants found:

• chr9-117681501-G-A
• chr9-117681501-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 0.822 in 151,468 control chromosomes in the GnomAD database, including 51,462 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 0.82 (51462 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.05
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.855 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.822 AC: 124426 AN: 151350 Hom.: 51415 Cov.: 32

Gnomad AFR AF: 0.767

Gnomad AMI AF: 0.876

Gnomad AMR AF: 0.868

Gnomad ASJ AF: 0.838

Gnomad EAS AF: 0.752

Gnomad SAS AF: 0.873

Gnomad FIN AF: 0.721

Gnomad MID AF: 0.847

Gnomad NFE AF: 0.861

Gnomad OTH AF: 0.838

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

GnomAD4 genome AF: 0.822 AC: 124531 AN: 151468 Hom.: 51462 Cov.: 32 AF XY: 0.818 AC XY: 60498 AN XY: 73978

African (AFR) AF: 0.767 AC: 31769 AN: 41424

American (AMR) AF: 0.868 AC: 13150 AN: 15154

Ashkenazi Jewish (ASJ) AF: 0.838 AC: 2898 AN: 3458

East Asian (EAS) AF: 0.752 AC: 3854 AN: 5126

South Asian (SAS) AF: 0.873 AC: 4206 AN: 4820

European-Finnish (FIN) AF: 0.721 AC: 7621 AN: 10570

Middle Eastern (MID) AF: 0.853 AC: 249 AN: 292

European-Non Finnish (NFE) AF: 0.861 AC: 58219 AN: 67606

Other (OTH) AF: 0.839 AC: 1766 AN: 2106

Alfa AF: 0.849 Hom.: 127792

Bravo AF: 0.829

Asia WGS AF: 0.831 AC: 2885 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	5.1
DANN	Benign	0.19
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs960312; hg19: chr9-120443779;