9-32792306-C-T

Variant names:

• chr9-32792306-C-T
• rs300634

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 0.599 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.450 AC: 18644 AN: 41474

American (AMR) AF: 0.581 AC: 8867 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.794 AC: 2756 AN: 3472

East Asian (EAS) AF: 0.664 AC: 3427 AN: 5164

South Asian (SAS) AF: 0.727 AC: 3498 AN: 4814

European-Finnish (FIN) AF: 0.615 AC: 6500 AN: 10570

Middle Eastern (MID) AF: 0.752 AC: 221 AN: 294

European-Non Finnish (NFE) AF: 0.666 AC: 45259 AN: 67982

Other (OTH) AF: 0.664 AC: 1401 AN: 2110

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
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs300634; hg19: chr9-32792304;