rs9457532

Positions:

• chr6-158931837-C-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 0.0315 in 151,104 control chromosomes in the GnomAD database, including 144 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 0.031 (144 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.212

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0512 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: 0.0315 AC: 4750 AN: 150986 Hom.: 144 Cov.: 32

Gnomad AFR AF: 0.0531

Gnomad AMI AF: 0.0943

Gnomad AMR AF: 0.0295

Gnomad ASJ AF: 0.00950

Gnomad EAS AF: 0.000215

Gnomad SAS AF: 0.0107

Gnomad FIN AF: 0.0162

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0251

Gnomad OTH AF: 0.0245

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

GnomAD4 genome AF: 0.0315 AC: 4758 AN: 151104 Hom.: 144 Cov.: 32 AF XY: 0.0301 AC XY: 2218 AN XY: 73720

Gnomad4 AFR AF: 0.0531

Gnomad4 AMR AF: 0.0295

Gnomad4 ASJ AF: 0.00950

Gnomad4 EAS AF: 0.000215

Gnomad4 SAS AF: 0.0107

Gnomad4 FIN AF: 0.0162

Gnomad4 NFE AF: 0.0252

Gnomad4 OTH AF: 0.0243

Alfa AF: 0.0272 Hom.: 16

Bravo AF: 0.0329

Asia WGS AF: 0.0140 AC: 46 AN: 3276

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.74
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9457532; hg19: chr6-159352869;