rs10489087

Variant names:

• chr4-13792792-G-A
• rs10489087
• ENST00000510907.5:n.282-36988G>A

Variant summary

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

The ENST00000510907.5(LINC01182):​n.282-36988G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.147 in 151,928 control chromosomes in the GnomAD database, including 1,823 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 0.15 (1823 hom., cov: 33)
• Consequence: LINC01182 ENST00000510907.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.877
• Publications: 10 publications found

Genes affected

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

ENSG00000288951 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.224 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01182	NR_121681.1	n.282-36988G>A		intron_variant	Intron 2 of 3
LOC101929048	XR_001741385.2	n.303-5666C>T		intron_variant	Intron 2 of 3
LOC101929048	XR_001741386.2	n.303-7099C>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01182	ENST00000510907.5	n.282-36988G>A		intron_variant	Intron 2 of 3	2
LINC01182	ENST00000669061.1	n.549-36988G>A		intron_variant	Intron 2 of 4
ENSG00000288951	ENST00000689499.3	n.193-25832C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.147 AC: 22351 AN: 151810 Hom.: 1815 Cov.: 33

Gnomad AFR AF: 0.158

Gnomad AMI AF: 0.269

Gnomad AMR AF: 0.230

Gnomad ASJ AF: 0.126

Gnomad EAS AF: 0.157

Gnomad SAS AF: 0.187

Gnomad FIN AF: 0.151

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.174

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

GnomAD4 genome AF: 0.147 AC: 22384 AN: 151928 Hom.: 1823 Cov.: 33 AF XY: 0.153 AC XY: 11348 AN XY: 74274

African (AFR) AF: 0.158 AC: 6563 AN: 41466

American (AMR) AF: 0.230 AC: 3508 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.126 AC: 438 AN: 3466

East Asian (EAS) AF: 0.156 AC: 810 AN: 5178

South Asian (SAS) AF: 0.187 AC: 900 AN: 4808

European-Finnish (FIN) AF: 0.151 AC: 1593 AN: 10544

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.117 AC: 7916 AN: 67914

Other (OTH) AF: 0.176 AC: 372 AN: 2110

Alfa AF: 0.130 Hom.: 5241

Bravo AF: 0.156

Asia WGS AF: 0.189 AC: 658 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.9
DANN	Benign	0.54
PhyloP100		0.88

Splicing

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

Other links and lift over

dbSNP: rs10489087; hg19: chr4-13794416;