chr9-25368390-G-T

Variant names:

• chr9-25368390-G-T
• rs10122848

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 0.211 in 151,992 control chromosomes in the GnomAD database, including 3,794 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 0.21 (3794 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.29
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.362 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: 0.211 AC: 31983 AN: 151874 Hom.: 3792 Cov.: 32

Gnomad AFR AF: 0.297

Gnomad AMI AF: 0.0779

Gnomad AMR AF: 0.124

Gnomad ASJ AF: 0.165

Gnomad EAS AF: 0.377

Gnomad SAS AF: 0.205

Gnomad FIN AF: 0.244

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.165

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.211 AC: 32007 AN: 151992 Hom.: 3794 Cov.: 32 AF XY: 0.214 AC XY: 15896 AN XY: 74264

African (AFR) AF: 0.297 AC: 12311 AN: 41458

American (AMR) AF: 0.123 AC: 1885 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.165 AC: 572 AN: 3470

East Asian (EAS) AF: 0.376 AC: 1933 AN: 5146

South Asian (SAS) AF: 0.205 AC: 991 AN: 4824

European-Finnish (FIN) AF: 0.244 AC: 2572 AN: 10558

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.165 AC: 11191 AN: 67956

Other (OTH) AF: 0.200 AC: 422 AN: 2108

Alfa AF: 0.171 Hom.: 9273

Bravo AF: 0.205

Asia WGS AF: 0.230 AC: 801 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.046
DANN	Benign	0.19
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs10122848; hg19: chr9-25368388; COSMIC: COSV60344665;