rs12592330

Variant names:

• chr15-48353083-T-C
• rs12592330

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 0.178 in 152,034 control chromosomes in the GnomAD database, including 2,658 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 0.18 (2658 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0640
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.394 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: 0.178 AC: 27098 AN: 151916 Hom.: 2653 Cov.: 31

Gnomad AFR AF: 0.189

Gnomad AMI AF: 0.0932

Gnomad AMR AF: 0.189

Gnomad ASJ AF: 0.182

Gnomad EAS AF: 0.409

Gnomad SAS AF: 0.215

Gnomad FIN AF: 0.136

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.157

Gnomad OTH AF: 0.193

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

GnomAD4 genome AF: 0.178 AC: 27134 AN: 152034 Hom.: 2658 Cov.: 31 AF XY: 0.179 AC XY: 13287 AN XY: 74342

African (AFR) AF: 0.189 AC: 7819 AN: 41462

American (AMR) AF: 0.189 AC: 2890 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.182 AC: 632 AN: 3472

East Asian (EAS) AF: 0.409 AC: 2112 AN: 5166

South Asian (SAS) AF: 0.214 AC: 1031 AN: 4810

European-Finnish (FIN) AF: 0.136 AC: 1433 AN: 10570

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.157 AC: 10661 AN: 67958

Other (OTH) AF: 0.199 AC: 418 AN: 2104

Alfa AF: 0.167 Hom.: 538

Bravo AF: 0.182

Asia WGS AF: 0.320 AC: 1109 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.9
DANN	Benign	0.84
PhyloP100		-0.064

Splicing

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

Other links and lift over

dbSNP: rs12592330; hg19: chr15-48645280;