chr9-117684548-C-T

Position:

• chr9-117684548-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 0.527 in 151,698 control chromosomes in the GnomAD database, including 23,738 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 0.53 (23738 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.475

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.662 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: 0.528 AC: 80010 AN: 151580 Hom.: 23744 Cov.: 32

Gnomad AFR AF: 0.234

Gnomad AMI AF: 0.758

Gnomad AMR AF: 0.586

Gnomad ASJ AF: 0.617

Gnomad EAS AF: 0.618

Gnomad SAS AF: 0.613

Gnomad FIN AF: 0.554

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.667

Gnomad OTH AF: 0.574

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

GnomAD4 genome AF: 0.527 AC: 80018 AN: 151698 Hom.: 23738 Cov.: 32 AF XY: 0.526 AC XY: 38999 AN XY: 74134

Gnomad4 AFR AF: 0.234

Gnomad4 AMR AF: 0.586

Gnomad4 ASJ AF: 0.617

Gnomad4 EAS AF: 0.618

Gnomad4 SAS AF: 0.612

Gnomad4 FIN AF: 0.554

Gnomad4 NFE AF: 0.667

Gnomad4 OTH AF: 0.571

Alfa AF: 0.632 Hom.: 14137

Bravo AF: 0.520

Asia WGS AF: 0.589 AC: 2050 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.45
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1928298; hg19: chr9-120446826;