ENST00000553818.1:n.489-18457T>G

Variant names:

• chr15-93779584-A-C
• rs12439760
• ENST00000553818.1:n.489-18457T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000553818.1(LINC01579):​n.489-18457T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: LINC01579 ENST00000553818.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.129
• Publications: 1 publications found

Genes affected

LINC01579 (HGNC:27519): (long intergenic non-protein coding RNA 1579)

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 = 0.247 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
LINC01579	ENST00000553818.1	n.489-18457T>G		intron_variant	Intron 3 of 3	4
LINC01579	ENST00000557481.6	n.541-18457T>G		intron_variant	Intron 4 of 6	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

African (AFR) AF: 0.134 AC: 5562 AN: 41470

American (AMR) AF: 0.194 AC: 2959 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.205 AC: 712 AN: 3468

East Asian (EAS) AF: 0.258 AC: 1325 AN: 5130

South Asian (SAS) AF: 0.0892 AC: 429 AN: 4810

European-Finnish (FIN) AF: 0.204 AC: 2146 AN: 10540

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.182 AC: 12351 AN: 67964

Other (OTH) AF: 0.191 AC: 403 AN: 2110

Alfa AF: 0.180 Hom.: 3047

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
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs12439760; hg19: chr15-94322813;