rs9296015

Variant names:

• chr6-32251212-G-A
• rs9296015

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 48 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.237 AC: 9829 AN: 41438

American (AMR) AF: 0.246 AC: 3761 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.219 AC: 759 AN: 3466

East Asian (EAS) AF: 0.315 AC: 1625 AN: 5162

South Asian (SAS) AF: 0.194 AC: 932 AN: 4808

European-Finnish (FIN) AF: 0.292 AC: 3076 AN: 10530

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.180 AC: 12243 AN: 67974

Other (OTH) AF: 0.236 AC: 499 AN: 2110

Alfa AF: 0.191 Hom.: 11596

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
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs9296015; hg19: chr6-32218989;