rs9296015

chr6-32251212-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 0.217 in 151,958 control chromosomes in the GnomAD database, including 3,805 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 0.22 (3805 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.327

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.302 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.217 AC: 32906 AN: 151840 Hom.: 3794 Cov.: 31

Gnomad AFR AF: 0.237

Gnomad AMI AF: 0.178

Gnomad AMR AF: 0.247

Gnomad ASJ AF: 0.219

Gnomad EAS AF: 0.315

Gnomad SAS AF: 0.193

Gnomad FIN AF: 0.292

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.180

Gnomad OTH AF: 0.229

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

GnomAD4 genome AF: 0.217 AC: 32942 AN: 151958 Hom.: 3805 Cov.: 31 AF XY: 0.221 AC XY: 16422 AN XY: 74252

Gnomad4 AFR AF: 0.237

Gnomad4 AMR AF: 0.246

Gnomad4 ASJ AF: 0.219

Gnomad4 EAS AF: 0.315

Gnomad4 SAS AF: 0.194

Gnomad4 FIN AF: 0.292

Gnomad4 NFE AF: 0.180

Gnomad4 OTH AF: 0.236

Alfa AF: 0.186 Hom.: 4221

Bravo AF: 0.215

Asia WGS AF: 0.314 AC: 1090 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	3.6
Dann	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9296015; hg19: chr6-32218989;