rs9327332

Variant names:

• chr5-124553888-A-C
• rs9327332

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 0.149 in 152,158 control chromosomes in the GnomAD database, including 1,728 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 0.15 (1728 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.584

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.169 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: 0.149 AC: 22580 AN: 152040 Hom.: 1723 Cov.: 33

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.112

Gnomad ASJ AF: 0.170

Gnomad EAS AF: 0.0462

Gnomad SAS AF: 0.0972

Gnomad FIN AF: 0.126

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.172

Gnomad OTH AF: 0.148

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

GnomAD4 genome AF: 0.149 AC: 22603 AN: 152158 Hom.: 1728 Cov.: 33 AF XY: 0.143 AC XY: 10645 AN XY: 74374

Gnomad4 AFR AF: 0.148

Gnomad4 AMR AF: 0.111

Gnomad4 ASJ AF: 0.170

Gnomad4 EAS AF: 0.0461

Gnomad4 SAS AF: 0.0964

Gnomad4 FIN AF: 0.126

Gnomad4 NFE AF: 0.172

Gnomad4 OTH AF: 0.146

Alfa AF: 0.163 Hom.: 973

Bravo AF: 0.150

Asia WGS AF: 0.0870 AC: 304 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	12
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9327332; hg19: chr5-123889581;