18-6550118-C-T

Variant names:

• chr18-6550118-C-T
• rs4411591
• ENST00000584361.1:n.284-25872C>T

Variant summary

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

The ENST00000584361.1(LINC01387):​n.284-25872C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.131 in 152,346 control chromosomes in the GnomAD database, including 1,887 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 0.13 (1887 hom., cov: 34)
• Consequence: LINC01387 ENST00000584361.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.282
• Publications: 14 publications found

Genes affected

LINC01387 (HGNC:44660): (long intergenic non-protein coding RNA 1387)

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 (NFE) allele frequency at 95% confidence interval = 0.193 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01387	NR_120518.1	n.284-25872C>T		intron_variant	Intron 2 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01387	ENST00000584361.1	n.284-25872C>T		intron_variant	Intron 2 of 5	3
LINC01387	ENST00000756158.1	n.308-25872C>T		intron_variant	Intron 3 of 4
LINC01387	ENST00000756159.1	n.227-25872C>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.132 AC: 20027 AN: 152228 Hom.: 1888 Cov.: 34

Gnomad AFR AF: 0.0306

Gnomad AMI AF: 0.253

Gnomad AMR AF: 0.100

Gnomad ASJ AF: 0.131

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0583

Gnomad FIN AF: 0.246

Gnomad MID AF: 0.0669

Gnomad NFE AF: 0.196

Gnomad OTH AF: 0.135

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

GnomAD4 genome AF: 0.131 AC: 20024 AN: 152346 Hom.: 1887 Cov.: 34 AF XY: 0.131 AC XY: 9728 AN XY: 74482

African (AFR) AF: 0.0305 AC: 1270 AN: 41598

American (AMR) AF: 0.0999 AC: 1530 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.131 AC: 454 AN: 3472

East Asian (EAS) AF: 0.000578 AC: 3 AN: 5190

South Asian (SAS) AF: 0.0582 AC: 281 AN: 4832

European-Finnish (FIN) AF: 0.246 AC: 2611 AN: 10606

Middle Eastern (MID) AF: 0.0719 AC: 21 AN: 292

European-Non Finnish (NFE) AF: 0.196 AC: 13341 AN: 68022

Other (OTH) AF: 0.133 AC: 282 AN: 2114

Alfa AF: 0.0743 Hom.: 211

Bravo AF: 0.115

Asia WGS AF: 0.0250 AC: 88 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	3.6
DANN	Benign	0.62
PhyloP100		0.28
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs4411591; hg19: chr18-6550117;