18-10616083-T-C

Variant names:

• chr18-10616083-T-C
• rs509049
• ENST00000583691.2:n.380+752A>G

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000584734.2(LINC01887):​n.1880+750A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.38 (549 hom., cov: 5)
  • Failed GnomAD Quality Control
• Consequence: LINC01887 ENST00000584734.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.257
• Publications: 1 publications found

Genes affected

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

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01887	NR_146509.1		n.388+739A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01887	ENST00000583691.2	TSL:5	n.380+752A>G		intron	N/A
	LINC01887	ENST00000584734.2	TSL:3	n.1880+750A>G		intron	N/A
	LINC01887	ENST00000743532.1		n.382+750A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.376 AC: 15072 AN: 40064 Hom.: 548 Cov.: 5

Gnomad AFR AF: 0.248

Gnomad AMI AF: 0.359

Gnomad AMR AF: 0.399

Gnomad ASJ AF: 0.460

Gnomad EAS AF: 0.460

Gnomad SAS AF: 0.407

Gnomad FIN AF: 0.276

Gnomad MID AF: 0.435

Gnomad NFE AF: 0.434

Gnomad OTH AF: 0.406

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

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.376 AC: 15065 AN: 40094 Hom.: 549 Cov.: 5 AF XY: 0.367 AC XY: 6881 AN XY: 18726

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.248 AC: 2564 AN: 10350

American (AMR) AF: 0.399 AC: 1398 AN: 3502

Ashkenazi Jewish (ASJ) AF: 0.460 AC: 475 AN: 1032

East Asian (EAS) AF: 0.461 AC: 576 AN: 1250

South Asian (SAS) AF: 0.405 AC: 482 AN: 1190

European-Finnish (FIN) AF: 0.276 AC: 468 AN: 1694

Middle Eastern (MID) AF: 0.427 AC: 35 AN: 82

European-Non Finnish (NFE) AF: 0.434 AC: 8769 AN: 20224

Other (OTH) AF: 0.405 AC: 191 AN: 472

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.38
DANN	Benign	0.43
PhyloP100		0.26

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs509049;

hg19: chr18-10616080;