chr9-128148408-A-G

Position:

• chr9-128148408-A-G

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 0.0761 in 152,254 control chromosomes in the GnomAD database, including 858 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 0.076 (858 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.76

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.423 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0762 AC: 11594 AN: 152136 Hom.: 861 Cov.: 31

Gnomad AFR AF: 0.0935

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0527

Gnomad ASJ AF: 0.0317

Gnomad EAS AF: 0.439

Gnomad SAS AF: 0.107

Gnomad FIN AF: 0.0840

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0435

Gnomad OTH AF: 0.0689

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

GnomAD4 genome AF: 0.0761 AC: 11584 AN: 152254 Hom.: 858 Cov.: 31 AF XY: 0.0799 AC XY: 5947 AN XY: 74438

Gnomad4 AFR AF: 0.0933

Gnomad4 AMR AF: 0.0527

Gnomad4 ASJ AF: 0.0317

Gnomad4 EAS AF: 0.438

Gnomad4 SAS AF: 0.106

Gnomad4 FIN AF: 0.0840

Gnomad4 NFE AF: 0.0435

Gnomad4 OTH AF: 0.0687

Alfa AF: 0.0503 Hom.: 755

Bravo AF: 0.0766

Asia WGS AF: 0.227 AC: 787 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	13
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3814526; hg19: chr9-130910687;