rs9404502

Variant names:

• chr6-104051246-C-A
• rs9404502

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 0.135 in 151,854 control chromosomes in the GnomAD database, including 1,524 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 0.14 (1524 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.540

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.184 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: 0.135 AC: 20542 AN: 151738 Hom.: 1519 Cov.: 32

Gnomad AFR AF: 0.0911

Gnomad AMI AF: 0.0714

Gnomad AMR AF: 0.190

Gnomad ASJ AF: 0.165

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.177

Gnomad FIN AF: 0.0635

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.155

Gnomad OTH AF: 0.169

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

GnomAD4 genome AF: 0.135 AC: 20555 AN: 151854 Hom.: 1524 Cov.: 32 AF XY: 0.133 AC XY: 9863 AN XY: 74224

Gnomad4 AFR AF: 0.0910

Gnomad4 AMR AF: 0.190

Gnomad4 ASJ AF: 0.165

Gnomad4 EAS AF: 0.152

Gnomad4 SAS AF: 0.178

Gnomad4 FIN AF: 0.0635

Gnomad4 NFE AF: 0.155

Gnomad4 OTH AF: 0.171

Alfa AF: 0.160 Hom.: 2567

Bravo AF: 0.142

Asia WGS AF: 0.147 AC: 513 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	8.1
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9404502; hg19: chr6-104499121;