rs3928291

Positions:

• chr9-129414472-G-A

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 0.139 in 152,174 control chromosomes in the GnomAD database, including 1,954 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 (1954 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.435

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.305 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.139 AC: 21206 AN: 152056 Hom.: 1956 Cov.: 32

Gnomad AFR AF: 0.0359

Gnomad AMI AF: 0.0855

Gnomad AMR AF: 0.148

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.167

Gnomad SAS AF: 0.319

Gnomad FIN AF: 0.146

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.184

Gnomad OTH AF: 0.136

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

GnomAD4 genome AF: 0.139 AC: 21198 AN: 152174 Hom.: 1954 Cov.: 32 AF XY: 0.141 AC XY: 10501 AN XY: 74382

Gnomad4 AFR AF: 0.0357

Gnomad4 AMR AF: 0.149

Gnomad4 ASJ AF: 0.163

Gnomad4 EAS AF: 0.166

Gnomad4 SAS AF: 0.318

Gnomad4 FIN AF: 0.146

Gnomad4 NFE AF: 0.184

Gnomad4 OTH AF: 0.135

Alfa AF: 0.174 Hom.: 3254

Bravo AF: 0.130

Asia WGS AF: 0.195 AC: 680 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	3.9
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3928291; hg19: chr9-132176751; COSMIC: COSV60402868;