15-33230084-A-G

Variant names:

• chr15-33230084-A-G
• rs12443212

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 0.193 in 152,138 control chromosomes in the GnomAD database, including 3,154 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 0.19 (3154 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.52
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.357 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.193 AC: 29404 AN: 152020 Hom.: 3149 Cov.: 32

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.110

Gnomad AMR AF: 0.317

Gnomad ASJ AF: 0.143

Gnomad EAS AF: 0.370

Gnomad SAS AF: 0.252

Gnomad FIN AF: 0.256

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.191

Gnomad OTH AF: 0.186

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

GnomAD4 genome AF: 0.193 AC: 29414 AN: 152138 Hom.: 3154 Cov.: 32 AF XY: 0.201 AC XY: 14968 AN XY: 74358

African (AFR) AF: 0.113 AC: 4712 AN: 41536

American (AMR) AF: 0.317 AC: 4839 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.143 AC: 495 AN: 3470

East Asian (EAS) AF: 0.370 AC: 1920 AN: 5184

South Asian (SAS) AF: 0.252 AC: 1213 AN: 4818

European-Finnish (FIN) AF: 0.256 AC: 2694 AN: 10542

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.191 AC: 13003 AN: 67996

Other (OTH) AF: 0.188 AC: 397 AN: 2112

Alfa AF: 0.195 Hom.: 5913

Bravo AF: 0.195

Asia WGS AF: 0.325 AC: 1125 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	7.1
DANN	Benign	0.76
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs12443212; hg19: chr15-33522285;