rs16889099

Variant names:

• chr4-13730462-T-C
• rs16889099
• ENST00000510907.5:n.281+72608T>C

Variant summary

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

The ENST00000510907.5(LINC01182):​n.281+72608T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.089 in 152,220 control chromosomes in the GnomAD database, including 615 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 0.089 (615 hom., cov: 32)
• Consequence: LINC01182 ENST00000510907.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.915
• Publications: 0 publications found

Genes affected

LINC01182 (HGNC:49564): (long intergenic non-protein coding RNA 1182)

ENSG00000306374 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.116 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000510907.5. 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
	LINC01182	NR_121681.1		n.281+72608T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01182	ENST00000510907.5	TSL:2	n.281+72608T>C		intron	N/A
	LINC01182	ENST00000669061.1		n.548+72608T>C		intron	N/A
	LINC01182	ENST00000715489.1		n.281+72608T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0890 AC: 13535 AN: 152102 Hom.: 613 Cov.: 32

Gnomad AFR AF: 0.0861

Gnomad AMI AF: 0.146

Gnomad AMR AF: 0.0915

Gnomad ASJ AF: 0.0957

Gnomad EAS AF: 0.124

Gnomad SAS AF: 0.0976

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.0798

Gnomad OTH AF: 0.101

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

GnomAD4 genome AF: 0.0890 AC: 13553 AN: 152220 Hom.: 615 Cov.: 32 AF XY: 0.0920 AC XY: 6846 AN XY: 74428

African (AFR) AF: 0.0861 AC: 3579 AN: 41550

American (AMR) AF: 0.0918 AC: 1405 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0957 AC: 332 AN: 3470

East Asian (EAS) AF: 0.124 AC: 644 AN: 5178

South Asian (SAS) AF: 0.0979 AC: 471 AN: 4810

European-Finnish (FIN) AF: 0.124 AC: 1310 AN: 10602

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.0799 AC: 5430 AN: 67996

Other (OTH) AF: 0.101 AC: 212 AN: 2108

Alfa AF: 0.0847 Hom.: 715

Bravo AF: 0.0865

Asia WGS AF: 0.105 AC: 364 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	8.2
DANN	Benign	0.72
PhyloP100		0.92

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: rs16889099;

hg19: chr4-13732086;