ENST00000442182.3:n.384+5777G>A

Variant names:

• chr1-117302410-G-A
• rs1289830
• ENST00000442182.3:n.384+5777G>A

Variant summary

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

The ENST00000442182.3(LINC01525):​n.384+5777G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.713 in 152,114 control chromosomes in the GnomAD database, including 39,619 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 0.71 (39619 hom., cov: 32)
• Consequence: LINC01525 ENST00000442182.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.15
• Publications: 4 publications found

Genes affected

LINC01525 (HGNC:51264): (long intergenic non-protein coding RNA 1525)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.868 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01525	NR_126408.1	n.352+5777G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01525	ENST00000442182.3	n.384+5777G>A		intron_variant	Intron 2 of 2	2
LINC01525	ENST00000657479.2	n.542+5609G>A		intron_variant	Intron 2 of 2
LINC01525	ENST00000664471.1	n.217+5777G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.713 AC: 108410 AN: 151996 Hom.: 39600 Cov.: 32

Gnomad AFR AF: 0.558

Gnomad AMI AF: 0.819

Gnomad AMR AF: 0.672

Gnomad ASJ AF: 0.673

Gnomad EAS AF: 0.890

Gnomad SAS AF: 0.778

Gnomad FIN AF: 0.879

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.774

Gnomad OTH AF: 0.703

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

GnomAD4 genome AF: 0.713 AC: 108469 AN: 152114 Hom.: 39619 Cov.: 32 AF XY: 0.718 AC XY: 53382 AN XY: 74348

African (AFR) AF: 0.558 AC: 23148 AN: 41474

American (AMR) AF: 0.672 AC: 10264 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.673 AC: 2334 AN: 3470

East Asian (EAS) AF: 0.890 AC: 4606 AN: 5176

South Asian (SAS) AF: 0.778 AC: 3745 AN: 4814

European-Finnish (FIN) AF: 0.879 AC: 9303 AN: 10586

Middle Eastern (MID) AF: 0.643 AC: 189 AN: 294

European-Non Finnish (NFE) AF: 0.774 AC: 52642 AN: 67996

Other (OTH) AF: 0.707 AC: 1493 AN: 2112

Alfa AF: 0.744 Hom.: 81291

Bravo AF: 0.692

Asia WGS AF: 0.811 AC: 2822 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	13
DANN	Benign	0.64
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs1289830; hg19: chr1-117845032;