rs12148769

Variant names:

• chr15-23906947-G-A
• rs12148769

Your query was ambiguous. Multiple possible variants found:

• chr15-23906947-G-A
• chr15-23906947-G-T

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 0.0941 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

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 (EAS) allele frequency at 95% confidence interval = 0.314 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: 0.0942 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

Gnomad4 AFR AF: 0.0260

Gnomad4 AMR AF: 0.169

Gnomad4 ASJ AF: 0.0756

Gnomad4 EAS AF: 0.326

Gnomad4 SAS AF: 0.188

Gnomad4 FIN AF: 0.0839

Gnomad4 NFE AF: 0.0966

Gnomad4 OTH AF: 0.100

Alfa AF: 0.101 Hom.: 1914

Bravo AF: 0.0996

Asia WGS AF: 0.245 AC: 852 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12148769; hg19: chr15-24152094;