9-12165758-G-T

Variant names:

• chr9-12165758-G-T
• rs7025259

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 0.869 in 152,160 control chromosomes in the GnomAD database, including 58,499 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 0.87 (58499 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0670
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.931 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: 0.869 AC: 132136 AN: 152044 Hom.: 58465 Cov.: 33

Gnomad AFR AF: 0.851

Gnomad AMI AF: 0.879

Gnomad AMR AF: 0.729

Gnomad ASJ AF: 0.952

Gnomad EAS AF: 0.442

Gnomad SAS AF: 0.743

Gnomad FIN AF: 0.937

Gnomad MID AF: 0.943

Gnomad NFE AF: 0.937

Gnomad OTH AF: 0.872

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

GnomAD4 genome AF: 0.869 AC: 132210 AN: 152160 Hom.: 58499 Cov.: 33 AF XY: 0.861 AC XY: 64047 AN XY: 74396

African (AFR) AF: 0.851 AC: 35318 AN: 41508

American (AMR) AF: 0.729 AC: 11132 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.952 AC: 3302 AN: 3470

East Asian (EAS) AF: 0.442 AC: 2273 AN: 5142

South Asian (SAS) AF: 0.745 AC: 3597 AN: 4828

European-Finnish (FIN) AF: 0.937 AC: 9935 AN: 10604

Middle Eastern (MID) AF: 0.946 AC: 278 AN: 294

European-Non Finnish (NFE) AF: 0.937 AC: 63758 AN: 68020

Other (OTH) AF: 0.861 AC: 1817 AN: 2110

Alfa AF: 0.907 Hom.: 235970

Bravo AF: 0.850

Asia WGS AF: 0.566 AC: 1972 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	4.6
DANN	Benign	0.61
PhyloP100		0.067

Splicing

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

Other links and lift over

dbSNP: rs7025259; hg19: chr9-12165758;