rs9332409

Variant names:

• chr5-30043316-C-A
• rs9332409

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 0.388 in 152,106 control chromosomes in the GnomAD database, including 12,298 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 0.39 (12298 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.78
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.757 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: 0.388 AC: 58990 AN: 151988 Hom.: 12280 Cov.: 33

Gnomad AFR AF: 0.308

Gnomad AMI AF: 0.375

Gnomad AMR AF: 0.467

Gnomad ASJ AF: 0.378

Gnomad EAS AF: 0.777

Gnomad SAS AF: 0.581

Gnomad FIN AF: 0.393

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.376

Gnomad OTH AF: 0.387

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

GnomAD4 genome AF: 0.388 AC: 59042 AN: 152106 Hom.: 12298 Cov.: 33 AF XY: 0.394 AC XY: 29318 AN XY: 74340

African (AFR) AF: 0.308 AC: 12802 AN: 41502

American (AMR) AF: 0.467 AC: 7148 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.378 AC: 1313 AN: 3470

East Asian (EAS) AF: 0.777 AC: 4015 AN: 5168

South Asian (SAS) AF: 0.580 AC: 2798 AN: 4824

European-Finnish (FIN) AF: 0.393 AC: 4146 AN: 10560

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.376 AC: 25553 AN: 67974

Other (OTH) AF: 0.391 AC: 826 AN: 2114

Alfa AF: 0.375 Hom.: 2287

Bravo AF: 0.386

Asia WGS AF: 0.695 AC: 2417 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.20
DANN	Benign	0.57
PhyloP100		-3.8

Splicing

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

Other links and lift over

dbSNP: rs9332409; hg19: chr5-30043423;