chr9-32793468-C-A

Variant names:

• chr9-32793468-C-A
• rs300622

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 0.792 in 152,182 control chromosomes in the GnomAD database, including 48,365 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 (48365 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.282
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.968 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: 0.793 AC: 120516 AN: 152064 Hom.: 48333 Cov.: 33

Gnomad AFR AF: 0.661

Gnomad AMI AF: 0.756

Gnomad AMR AF: 0.822

Gnomad ASJ AF: 0.892

Gnomad EAS AF: 0.991

Gnomad SAS AF: 0.885

Gnomad FIN AF: 0.860

Gnomad MID AF: 0.860

Gnomad NFE AF: 0.829

Gnomad OTH AF: 0.798

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

GnomAD4 genome AF: 0.792 AC: 120596 AN: 152182 Hom.: 48365 Cov.: 33 AF XY: 0.797 AC XY: 59343 AN XY: 74418

African (AFR) AF: 0.661 AC: 27398 AN: 41472

American (AMR) AF: 0.822 AC: 12574 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.892 AC: 3098 AN: 3472

East Asian (EAS) AF: 0.991 AC: 5142 AN: 5190

South Asian (SAS) AF: 0.885 AC: 4266 AN: 4820

European-Finnish (FIN) AF: 0.860 AC: 9118 AN: 10602

Middle Eastern (MID) AF: 0.853 AC: 249 AN: 292

European-Non Finnish (NFE) AF: 0.829 AC: 56372 AN: 68024

Other (OTH) AF: 0.801 AC: 1691 AN: 2112

Alfa AF: 0.816 Hom.: 27612

Bravo AF: 0.785

Asia WGS AF: 0.918 AC: 3192 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.2
DANN	Benign	0.37
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs300622; hg19: chr9-32793466;