9-32792306-C-T

Position:

• chr9-32792306-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 0.599 in 152,062 control chromosomes in the GnomAD database, including 28,040 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 0.60 (28040 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.707 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: 0.600 AC: 91130 AN: 151944 Hom.: 28046 Cov.: 32

Gnomad AFR AF: 0.450

Gnomad AMI AF: 0.631

Gnomad AMR AF: 0.580

Gnomad ASJ AF: 0.794

Gnomad EAS AF: 0.664

Gnomad SAS AF: 0.727

Gnomad FIN AF: 0.615

Gnomad MID AF: 0.769

Gnomad NFE AF: 0.666

Gnomad OTH AF: 0.663

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

GnomAD4 genome AF: 0.599 AC: 91147 AN: 152062 Hom.: 28040 Cov.: 32 AF XY: 0.600 AC XY: 44615 AN XY: 74334

Gnomad4 AFR AF: 0.450

Gnomad4 AMR AF: 0.581

Gnomad4 ASJ AF: 0.794

Gnomad4 EAS AF: 0.664

Gnomad4 SAS AF: 0.727

Gnomad4 FIN AF: 0.615

Gnomad4 NFE AF: 0.666

Gnomad4 OTH AF: 0.664

Alfa AF: 0.618 Hom.: 3677

Bravo AF: 0.591

Asia WGS AF: 0.682 AC: 2374 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	12
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs300634; hg19: chr9-32792304;