rs12148430

Variant names:

• chr15-26298579-C-G
• rs12148430

Your query was ambiguous. Multiple possible variants found:

• chr15-26298579-C-G
• chr15-26298579-C-T

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 0.15 in 152,168 control chromosomes in the GnomAD database, including 1,760 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 0.15 (1760 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.117
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.188 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: 0.150 AC: 22748 AN: 152050 Hom.: 1753 Cov.: 33

Gnomad AFR AF: 0.159

Gnomad AMI AF: 0.184

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.251

Gnomad EAS AF: 0.0866

Gnomad SAS AF: 0.198

Gnomad FIN AF: 0.141

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.148

Gnomad OTH AF: 0.152

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

GnomAD4 genome AF: 0.150 AC: 22786 AN: 152168 Hom.: 1760 Cov.: 33 AF XY: 0.151 AC XY: 11208 AN XY: 74394

African (AFR) AF: 0.160 AC: 6639 AN: 41538

American (AMR) AF: 0.116 AC: 1773 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.251 AC: 870 AN: 3470

East Asian (EAS) AF: 0.0868 AC: 448 AN: 5160

South Asian (SAS) AF: 0.199 AC: 957 AN: 4820

European-Finnish (FIN) AF: 0.141 AC: 1490 AN: 10584

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.148 AC: 10078 AN: 67994

Other (OTH) AF: 0.152 AC: 321 AN: 2110

Alfa AF: 0.0608 Hom.: 61

Bravo AF: 0.148

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.6
DANN	Benign	0.30
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs12148430; hg19: chr15-26543726;