9-32372464-C-T

Variant names:

• chr9-32372464-C-T
• rs7855483

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 0.788 in 152,226 control chromosomes in the GnomAD database, including 47,545 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 0.79 (47545 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.386
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.799 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: 0.788 AC: 119915 AN: 152108 Hom.: 47507 Cov.: 33

Gnomad AFR AF: 0.799

Gnomad AMI AF: 0.766

Gnomad AMR AF: 0.750

Gnomad ASJ AF: 0.767

Gnomad EAS AF: 0.707

Gnomad SAS AF: 0.624

Gnomad FIN AF: 0.818

Gnomad MID AF: 0.775

Gnomad NFE AF: 0.805

Gnomad OTH AF: 0.783

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

GnomAD4 genome AF: 0.788 AC: 120010 AN: 152226 Hom.: 47545 Cov.: 33 AF XY: 0.786 AC XY: 58500 AN XY: 74436

African (AFR) AF: 0.799 AC: 33186 AN: 41520

American (AMR) AF: 0.750 AC: 11471 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.767 AC: 2660 AN: 3470

East Asian (EAS) AF: 0.706 AC: 3651 AN: 5170

South Asian (SAS) AF: 0.626 AC: 3011 AN: 4812

European-Finnish (FIN) AF: 0.818 AC: 8686 AN: 10616

Middle Eastern (MID) AF: 0.769 AC: 226 AN: 294

European-Non Finnish (NFE) AF: 0.805 AC: 54766 AN: 68026

Other (OTH) AF: 0.783 AC: 1656 AN: 2114

Alfa AF: 0.798 Hom.: 31721

Bravo AF: 0.788

Asia WGS AF: 0.718 AC: 2497 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.77
DANN	Benign	0.16
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs7855483; hg19: chr9-32372462;