18-10626554-G-T

Variant names:

• chr18-10626554-G-T
• rs2276371
• ENST00000584734.2:n.1370C>A

Variant summary

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

The ENST00000584734.2(LINC01887):​n.1370C>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.41 in 152,094 control chromosomes in the GnomAD database, including 13,073 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 0.41 (13073 hom., cov: 32)
• Consequence: LINC01887 ENST00000584734.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.472
• Publications: 2 publications found

Genes affected

LINC01887 (HGNC:52706): (long intergenic non-protein coding RNA 1887)

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 (SAS) allele frequency at 95% confidence interval = 0.558 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000584734.2. 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
	LINC01887	NR_146509.1		n.-134C>A		upstream_gene	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01887	ENST00000584734.2	TSL:3	n.1370C>A		non_coding_transcript_exon	Exon 3 of 5
	LINC01887	ENST00000743550.1		n.91C>A		non_coding_transcript_exon	Exon 1 of 2
	LINC01887	ENST00000743551.1		n.117C>A		non_coding_transcript_exon	Exon 1 of 3

Frequencies

GnomAD3 genomes AF: 0.410 AC: 62331 AN: 151976 Hom.: 13063 Cov.: 32

Gnomad AFR AF: 0.320

Gnomad AMI AF: 0.361

Gnomad AMR AF: 0.481

Gnomad ASJ AF: 0.448

Gnomad EAS AF: 0.467

Gnomad SAS AF: 0.574

Gnomad FIN AF: 0.373

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.436

Gnomad OTH AF: 0.453

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

GnomAD4 genome AF: 0.410 AC: 62373 AN: 152094 Hom.: 13073 Cov.: 32 AF XY: 0.411 AC XY: 30555 AN XY: 74352

African (AFR) AF: 0.320 AC: 13262 AN: 41472

American (AMR) AF: 0.481 AC: 7354 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.448 AC: 1553 AN: 3466

East Asian (EAS) AF: 0.468 AC: 2418 AN: 5170

South Asian (SAS) AF: 0.576 AC: 2778 AN: 4822

European-Finnish (FIN) AF: 0.373 AC: 3949 AN: 10594

Middle Eastern (MID) AF: 0.545 AC: 159 AN: 292

European-Non Finnish (NFE) AF: 0.436 AC: 29617 AN: 67980

Other (OTH) AF: 0.452 AC: 954 AN: 2110

Alfa AF: 0.414 Hom.: 6367

Bravo AF: 0.412

Asia WGS AF: 0.544 AC: 1892 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.0
DANN	Benign	0.30
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs2276371; hg19: chr18-10626551; COSMIC: COSV73839434;