18-6505598-G-A

Variant names:

• chr18-6505598-G-A
• rs11873891
• ENST00000756158.1:n.81-3936G>A

Variant summary

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

The ENST00000756158.1(LINC01387):​n.81-3936G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.577 in 152,034 control chromosomes in the GnomAD database, including 25,834 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 0.58 (25834 hom., cov: 32)
• Consequence: LINC01387 ENST00000756158.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.392
• Publications: 3 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.642 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01387	ENST00000756158.1	n.81-3936G>A		intron_variant	Intron 1 of 4
LINC01387	ENST00000756159.1	n.88-3936G>A		intron_variant	Intron 1 of 3
LINC01387	ENST00000756160.1	n.216-3936G>A		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.577 AC: 87580 AN: 151916 Hom.: 25801 Cov.: 32

Gnomad AFR AF: 0.531

Gnomad AMI AF: 0.449

Gnomad AMR AF: 0.653

Gnomad ASJ AF: 0.628

Gnomad EAS AF: 0.311

Gnomad SAS AF: 0.394

Gnomad FIN AF: 0.587

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.617

Gnomad OTH AF: 0.598

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

GnomAD4 genome AF: 0.577 AC: 87657 AN: 152034 Hom.: 25834 Cov.: 32 AF XY: 0.569 AC XY: 42289 AN XY: 74310

African (AFR) AF: 0.531 AC: 22034 AN: 41482

American (AMR) AF: 0.653 AC: 9961 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.628 AC: 2179 AN: 3470

East Asian (EAS) AF: 0.311 AC: 1608 AN: 5168

South Asian (SAS) AF: 0.394 AC: 1898 AN: 4820

European-Finnish (FIN) AF: 0.587 AC: 6194 AN: 10558

Middle Eastern (MID) AF: 0.622 AC: 183 AN: 294

European-Non Finnish (NFE) AF: 0.617 AC: 41930 AN: 67964

Other (OTH) AF: 0.597 AC: 1261 AN: 2114

Alfa AF: 0.599 Hom.: 22830

Bravo AF: 0.582

Asia WGS AF: 0.384 AC: 1334 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	8.4
DANN	Benign	0.51
PhyloP100		0.39

Splicing

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

Other links and lift over

dbSNP: rs11873891; hg19: chr18-6505597;