rs9404952

Variant names:

• chr6-29836388-G-A
• rs9404952

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 0.468 in 152,016 control chromosomes in the GnomAD database, including 16,918 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 0.47 (16918 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.69

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.639 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: 0.468 AC: 71147 AN: 151898 Hom.: 16901 Cov.: 32

Gnomad AFR AF: 0.518

Gnomad AMI AF: 0.463

Gnomad AMR AF: 0.501

Gnomad ASJ AF: 0.392

Gnomad EAS AF: 0.658

Gnomad SAS AF: 0.397

Gnomad FIN AF: 0.460

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.427

Gnomad OTH AF: 0.464

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

GnomAD4 genome AF: 0.468 AC: 71197 AN: 152016 Hom.: 16918 Cov.: 32 AF XY: 0.467 AC XY: 34728 AN XY: 74288

Gnomad4 AFR AF: 0.518

Gnomad4 AMR AF: 0.502

Gnomad4 ASJ AF: 0.392

Gnomad4 EAS AF: 0.658

Gnomad4 SAS AF: 0.396

Gnomad4 FIN AF: 0.460

Gnomad4 NFE AF: 0.427

Gnomad4 OTH AF: 0.467

Alfa AF: 0.438 Hom.: 8789

Bravo AF: 0.477

Asia WGS AF: 0.543 AC: 1885 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	3.1
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9404952; hg19: chr6-29804165;