rs509049

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr18-10616083-T-A
• chr18-10616083-T-C

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>T 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 0.0 (0 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=-0.92).

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>T		intron	N/A

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.00 AC: 0 AN: 52636 Hom.: 0 Cov.: 5

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

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: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 52662 Hom.: 0 Cov.: 5 AF XY: 0.00 AC XY: 0 AN XY: 24666

African (AFR) AF: 0.00 AC: 0 AN: 13928

American (AMR) AF: 0.00 AC: 0 AN: 4616

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 1312

East Asian (EAS) AF: 0.00 AC: 0 AN: 1884

South Asian (SAS) AF: 0.00 AC: 0 AN: 1510

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2258

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 106

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 25988

Other (OTH) AF: 0.00 AC: 0 AN: 648

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	-0.92
CADD	Benign	0.31
DANN	Benign	0.41
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;