rs12439760

Positions:

• chr15-93779584-A-C
• chr15-93779584-A-G

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 0.172 in 151,962 control chromosomes in the GnomAD database, including 2,316 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 0.17 (2316 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.129

Genes affected

(HGNC:):

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 = 0.247 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.93779584A>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01579	ENST00000553818.1	n.489-18457T>G		intron_variant		4
LINC01579	ENST00000557481.6	n.541-18457T>G		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.172 AC: 26103 AN: 151846 Hom.: 2316 Cov.: 31

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.211

Gnomad AMR AF: 0.194

Gnomad ASJ AF: 0.205

Gnomad EAS AF: 0.258

Gnomad SAS AF: 0.0895

Gnomad FIN AF: 0.204

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.191

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

GnomAD4 genome AF: 0.172 AC: 26125 AN: 151962 Hom.: 2316 Cov.: 31 AF XY: 0.171 AC XY: 12709 AN XY: 74250

Gnomad4 AFR AF: 0.134

Gnomad4 AMR AF: 0.194

Gnomad4 ASJ AF: 0.205

Gnomad4 EAS AF: 0.258

Gnomad4 SAS AF: 0.0892

Gnomad4 FIN AF: 0.204

Gnomad4 NFE AF: 0.182

Gnomad4 OTH AF: 0.191

Alfa AF: 0.182 Hom.: 2199

Bravo AF: 0.174

Asia WGS AF: 0.159 AC: 553 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	2.8
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12439760; hg19: chr15-94322813;