ENST00000554318.2:n.325-24061T>C

Variant names:

• chr15-93736606-T-C
• rs4591081
• ENST00000554318.2:n.325-24061T>C

Variant summary

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

The ENST00000554318.2(ENSG00000257060):​n.325-24061T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.499 in 152,024 control chromosomes in the GnomAD database, including 19,224 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 0.50 (19224 hom., cov: 33)
• Consequence: ENSG00000257060 ENST00000554318.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.147
• Publications: 0 publications found

Genes affected

ENSG00000257060 (HGNC:):

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=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.65 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000554318.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000257060	ENST00000554318.2	TSL:3	n.325-24061T>C		intron	N/A
	LINC01579	ENST00000557481.6	TSL:5	n.1054-5255A>G		intron	N/A
	ENSG00000257060	ENST00000653322.2		n.1089-24061T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.499 AC: 75856 AN: 151908 Hom.: 19195 Cov.: 33

Gnomad AFR AF: 0.515

Gnomad AMI AF: 0.448

Gnomad AMR AF: 0.537

Gnomad ASJ AF: 0.537

Gnomad EAS AF: 0.468

Gnomad SAS AF: 0.668

Gnomad FIN AF: 0.507

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.469

Gnomad OTH AF: 0.487

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

GnomAD4 genome AF: 0.499 AC: 75933 AN: 152024 Hom.: 19224 Cov.: 33 AF XY: 0.507 AC XY: 37703 AN XY: 74318

African (AFR) AF: 0.516 AC: 21371 AN: 41446

American (AMR) AF: 0.538 AC: 8219 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.537 AC: 1863 AN: 3472

East Asian (EAS) AF: 0.468 AC: 2416 AN: 5162

South Asian (SAS) AF: 0.669 AC: 3228 AN: 4826

European-Finnish (FIN) AF: 0.507 AC: 5362 AN: 10582

Middle Eastern (MID) AF: 0.544 AC: 160 AN: 294

European-Non Finnish (NFE) AF: 0.469 AC: 31886 AN: 67942

Other (OTH) AF: 0.483 AC: 1020 AN: 2112

Alfa AF: 0.473 Hom.: 2060

Bravo AF: 0.496

Asia WGS AF: 0.571 AC: 1986 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.1
DANN	Benign	0.46
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs4591081; hg19: chr15-94279835;