ENST00000582386.4:n.674-1350A>G

Variant names:

• chr18-6567183-A-G
• rs948426
• ENST00000582386.4:n.674-1350A>G

Variant summary

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

The ENST00000582386.4(LINC01387):​n.674-1350A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.299 in 152,082 control chromosomes in the GnomAD database, including 8,782 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 0.30 (8782 hom., cov: 32)
• Consequence: LINC01387 ENST00000582386.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.149
• Publications: 8 publications found

Genes affected

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

LOC105371972 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.414 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000582386.4. 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
	LINC01387	NR_120518.1		n.284-8807A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01387	ENST00000582386.4	TSL:3	n.674-1350A>G		intron	N/A
	LINC01387	ENST00000584361.1	TSL:3	n.284-8807A>G		intron	N/A
	LINC01387	ENST00000684855.2		n.415-1350A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.299 AC: 45470 AN: 151964 Hom.: 8786 Cov.: 32

Gnomad AFR AF: 0.0744

Gnomad AMI AF: 0.436

Gnomad AMR AF: 0.309

Gnomad ASJ AF: 0.293

Gnomad EAS AF: 0.0684

Gnomad SAS AF: 0.351

Gnomad FIN AF: 0.487

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.419

Gnomad OTH AF: 0.281

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

GnomAD4 genome AF: 0.299 AC: 45466 AN: 152082 Hom.: 8782 Cov.: 32 AF XY: 0.300 AC XY: 22329 AN XY: 74326

African (AFR) AF: 0.0743 AC: 3086 AN: 41554

American (AMR) AF: 0.309 AC: 4717 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.293 AC: 1017 AN: 3468

East Asian (EAS) AF: 0.0686 AC: 355 AN: 5176

South Asian (SAS) AF: 0.351 AC: 1689 AN: 4810

European-Finnish (FIN) AF: 0.487 AC: 5135 AN: 10542

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.419 AC: 28432 AN: 67932

Other (OTH) AF: 0.277 AC: 584 AN: 2110

Alfa AF: 0.365 Hom.: 25703

Bravo AF: 0.274

Asia WGS AF: 0.192 AC: 670 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.6
DANN	Benign	0.53
PhyloP100		-0.15
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: rs948426; hg19: chr18-6567182;