chr9-125190369-A-T

Variant names:

• chr9-125190369-A-T
• rs458046

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 0.443 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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.476 AC: 19722 AN: 41396

American (AMR) AF: 0.370 AC: 5650 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.509 AC: 1765 AN: 3468

East Asian (EAS) AF: 0.537 AC: 2765 AN: 5152

South Asian (SAS) AF: 0.411 AC: 1978 AN: 4816

European-Finnish (FIN) AF: 0.293 AC: 3091 AN: 10558

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.453 AC: 30815 AN: 67954

Other (OTH) AF: 0.447 AC: 941 AN: 2106

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.0
DANN	Benign	0.61
PhyloP100		0.10
PromoterAI		0.029	Neutral

Splicing

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

Other links and lift over

dbSNP: rs458046; hg19: chr9-127952648;