chr9-25359815-T-G

Variant names:

• chr9-25359815-T-G
• rs7848925

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 0.255 in 151,846 control chromosomes in the GnomAD database, including 5,577 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 0.26 (5577 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.347
• Publications: 0 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 (EAS) allele frequency at 95% confidence interval = 0.396 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: 0.255 AC: 38714 AN: 151728 Hom.: 5570 Cov.: 32

Gnomad AFR AF: 0.384

Gnomad AMI AF: 0.0976

Gnomad AMR AF: 0.188

Gnomad ASJ AF: 0.181

Gnomad EAS AF: 0.411

Gnomad SAS AF: 0.230

Gnomad FIN AF: 0.248

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.189

Gnomad OTH AF: 0.244

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

GnomAD4 genome AF: 0.255 AC: 38748 AN: 151846 Hom.: 5577 Cov.: 32 AF XY: 0.257 AC XY: 19081 AN XY: 74210

African (AFR) AF: 0.385 AC: 15931 AN: 41420

American (AMR) AF: 0.188 AC: 2864 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.181 AC: 628 AN: 3468

East Asian (EAS) AF: 0.411 AC: 2120 AN: 5162

South Asian (SAS) AF: 0.230 AC: 1110 AN: 4820

European-Finnish (FIN) AF: 0.248 AC: 2615 AN: 10550

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.189 AC: 12819 AN: 67848

Other (OTH) AF: 0.241 AC: 509 AN: 2112

Alfa AF: 0.185 Hom.: 1514

Bravo AF: 0.260

Asia WGS AF: 0.254 AC: 884 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	7.1
DANN	Benign	0.78
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs7848925; hg19: chr9-25359813; COSMIC: COSV60344636;