15-23906947-G-A

Variant names:

• chr15-23906947-G-A
• rs12148769

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 0.0941 in 152,128 control chromosomes in the GnomAD database, including 1,026 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 0.094 (1026 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.351
• Publications: 20 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.314 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: 0.0942 AC: 14319 AN: 152010 Hom.: 1029 Cov.: 32

Gnomad AFR AF: 0.0260

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.169

Gnomad ASJ AF: 0.0756

Gnomad EAS AF: 0.327

Gnomad SAS AF: 0.188

Gnomad FIN AF: 0.0839

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.0966

Gnomad OTH AF: 0.0979

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

GnomAD4 genome AF: 0.0941 AC: 14317 AN: 152128 Hom.: 1026 Cov.: 32 AF XY: 0.0970 AC XY: 7216 AN XY: 74358

African (AFR) AF: 0.0260 AC: 1081 AN: 41508

American (AMR) AF: 0.169 AC: 2573 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0756 AC: 262 AN: 3464

East Asian (EAS) AF: 0.326 AC: 1688 AN: 5170

South Asian (SAS) AF: 0.188 AC: 903 AN: 4816

European-Finnish (FIN) AF: 0.0839 AC: 889 AN: 10590

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.0966 AC: 6566 AN: 67998

Other (OTH) AF: 0.100 AC: 211 AN: 2106

Alfa AF: 0.101 Hom.: 4403

Bravo AF: 0.0996

Asia WGS AF: 0.245 AC: 852 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.9
DANN	Benign	0.37
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs12148769; hg19: chr15-24152094;