9-25368390-G-T

Position:

• chr9-25368390-G-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.297

Gnomad4 AMR AF: 0.123

Gnomad4 ASJ AF: 0.165

Gnomad4 EAS AF: 0.376

Gnomad4 SAS AF: 0.205

Gnomad4 FIN AF: 0.244

Gnomad4 NFE AF: 0.165

Gnomad4 OTH AF: 0.200

Alfa AF: 0.159 Hom.: 3549

Bravo AF: 0.205

Asia WGS AF: 0.230 AC: 801 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

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