9-125190369-A-T

Variant names:

• chr9-125190369-A-T
• rs458046

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 0.443 in 151,900 control chromosomes in the GnomAD database, including 15,270 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 0.44 (15270 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.101

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.52 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.443 AC: 67213 AN: 151782 Hom.: 15249 Cov.: 31

Gnomad AFR AF: 0.476

Gnomad AMI AF: 0.469

Gnomad AMR AF: 0.371

Gnomad ASJ AF: 0.509

Gnomad EAS AF: 0.536

Gnomad SAS AF: 0.412

Gnomad FIN AF: 0.293

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.453

Gnomad OTH AF: 0.440

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

GnomAD4 genome AF: 0.443 AC: 67275 AN: 151900 Hom.: 15270 Cov.: 31 AF XY: 0.434 AC XY: 32203 AN XY: 74236

Gnomad4 AFR AF: 0.476

Gnomad4 AMR AF: 0.370

Gnomad4 ASJ AF: 0.509

Gnomad4 EAS AF: 0.537

Gnomad4 SAS AF: 0.411

Gnomad4 FIN AF: 0.293

Gnomad4 NFE AF: 0.453

Gnomad4 OTH AF: 0.447

Alfa AF: 0.280 Hom.: 639

Bravo AF: 0.452

Asia WGS AF: 0.498 AC: 1730 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.0
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs458046; hg19: chr9-127952648;