9-117530056-C-T

Position:

• chr9-117530056-C-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 0.482 in 152,032 control chromosomes in the GnomAD database, including 19,786 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 0.48 (19786 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0760

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 (NFE) allele frequency at 95% confidence interval = 0.609 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: 0.483 AC: 73300 AN: 151914 Hom.: 19785 Cov.: 32

Gnomad AFR AF: 0.267

Gnomad AMI AF: 0.743

Gnomad AMR AF: 0.390

Gnomad ASJ AF: 0.535

Gnomad EAS AF: 0.241

Gnomad SAS AF: 0.472

Gnomad FIN AF: 0.696

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.614

Gnomad OTH AF: 0.480

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

GnomAD4 genome AF: 0.482 AC: 73316 AN: 152032 Hom.: 19786 Cov.: 32 AF XY: 0.483 AC XY: 35881 AN XY: 74314

Gnomad4 AFR AF: 0.267

Gnomad4 AMR AF: 0.389

Gnomad4 ASJ AF: 0.535

Gnomad4 EAS AF: 0.241

Gnomad4 SAS AF: 0.472

Gnomad4 FIN AF: 0.696

Gnomad4 NFE AF: 0.614

Gnomad4 OTH AF: 0.475

Alfa AF: 0.575 Hom.: 52494

Bravo AF: 0.444

Asia WGS AF: 0.352 AC: 1229 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	3.0
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1985317; hg19: chr9-120292334;