ENST00000482617.4:n.199-14319C>A

Variant names:

• chr3-81080793-C-A
• rs17018482
• ENST00000482617.4:n.199-14319C>A

Variant summary

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

The ENST00000482617.4(LINC02027):​n.199-14319C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.188 in 152,074 control chromosomes in the GnomAD database, including 2,758 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 0.19 (2758 hom., cov: 32)
• Consequence: LINC02027 ENST00000482617.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.455
• Publications: 6 publications found

Genes affected

LINC02027 (HGNC:52862): (long intergenic non-protein coding RNA 2027)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.338 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02027	NR_132411.1	n.61-14319C>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02027	ENST00000482617.4	n.199-14319C>A		intron_variant	Intron 2 of 2	5
LINC02027	ENST00000653347.3	n.103-13840C>A		intron_variant	Intron 1 of 2
LINC02027	ENST00000662919.2	n.217-14319C>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.188 AC: 28525 AN: 151954 Hom.: 2748 Cov.: 32

Gnomad AFR AF: 0.186

Gnomad AMI AF: 0.0899

Gnomad AMR AF: 0.188

Gnomad ASJ AF: 0.115

Gnomad EAS AF: 0.351

Gnomad SAS AF: 0.232

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.178

Gnomad OTH AF: 0.186

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

GnomAD4 genome AF: 0.188 AC: 28561 AN: 152074 Hom.: 2758 Cov.: 32 AF XY: 0.189 AC XY: 14039 AN XY: 74326

African (AFR) AF: 0.187 AC: 7746 AN: 41484

American (AMR) AF: 0.189 AC: 2883 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.115 AC: 398 AN: 3472

East Asian (EAS) AF: 0.351 AC: 1806 AN: 5144

South Asian (SAS) AF: 0.232 AC: 1116 AN: 4812

European-Finnish (FIN) AF: 0.190 AC: 2013 AN: 10582

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.178 AC: 12081 AN: 67986

Other (OTH) AF: 0.187 AC: 393 AN: 2106

Alfa AF: 0.178 Hom.: 3298

Bravo AF: 0.190

Asia WGS AF: 0.282 AC: 983 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.67
DANN	Benign	0.66
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs17018482; hg19: chr3-81129944;