rs9327332

Variant names:

• chr5-124553888-A-C
• rs9327332

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 0.149 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
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• 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

African (AFR) AF: 0.148 AC: 6122 AN: 41498

American (AMR) AF: 0.111 AC: 1700 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.170 AC: 590 AN: 3472

East Asian (EAS) AF: 0.0461 AC: 239 AN: 5188

South Asian (SAS) AF: 0.0964 AC: 465 AN: 4822

European-Finnish (FIN) AF: 0.126 AC: 1331 AN: 10580

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.172 AC: 11695 AN: 68012

Other (OTH) AF: 0.146 AC: 309 AN: 2112

Alfa AF: 0.165 Hom.: 1109

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
PhyloP100		0.58

Splicing

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

Other links and lift over

dbSNP: rs9327332; hg19: chr5-123889581;