15-93736606-T-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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107983974	XR_001751681.2	n.1033-24061T>C		intron_variant	Intron 5 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000257060	ENST00000554318.2	n.325-24061T>C		intron_variant	Intron 3 of 3	3
LINC01579	ENST00000557481.6	n.1054-5255A>G		intron_variant	Intron 5 of 6	5
ENSG00000257060	ENST00000653322.2	n.1089-24061T>C		intron_variant	Intron 7 of 7

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 v4.3

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;