ENST00000587999.1:n.199-45349A>G

Variant names:

• chr17-68718141-A-G
• rs11658127
• ENST00000587999.1:n.199-45349A>G

Variant summary

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

The ENST00000587999.1(LINC01482):​n.199-45349A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.122 in 152,090 control chromosomes in the GnomAD database, including 1,173 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 0.12 (1173 hom., cov: 31)
• Consequence: LINC01482 ENST00000587999.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0950
• Publications: 5 publications found

Genes affected

LINC01482 (HGNC:51128): (long intergenic non-protein coding RNA 1482)

ENSG00000303167 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.218 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000587999.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01482	ENST00000587999.1	TSL:3	n.199-45349A>G		intron	N/A
	LINC01482	ENST00000589610.5	TSL:3	n.129-31974A>G		intron	N/A
	LINC01482	ENST00000792224.1		n.141+7207A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.122 AC: 18579 AN: 151972 Hom.: 1171 Cov.: 31

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.0493

Gnomad AMR AF: 0.105

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.228

Gnomad SAS AF: 0.167

Gnomad FIN AF: 0.0664

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.129

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

GnomAD4 genome AF: 0.122 AC: 18585 AN: 152090 Hom.: 1173 Cov.: 31 AF XY: 0.121 AC XY: 9015 AN XY: 74352

African (AFR) AF: 0.123 AC: 5107 AN: 41490

American (AMR) AF: 0.105 AC: 1604 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.161 AC: 557 AN: 3470

East Asian (EAS) AF: 0.229 AC: 1182 AN: 5158

South Asian (SAS) AF: 0.168 AC: 808 AN: 4812

European-Finnish (FIN) AF: 0.0664 AC: 703 AN: 10590

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.122 AC: 8270 AN: 67972

Other (OTH) AF: 0.130 AC: 274 AN: 2112

Alfa AF: 0.124 Hom.: 4742

Bravo AF: 0.121

Asia WGS AF: 0.203 AC: 705 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.4
DANN	Benign	0.57
PhyloP100		0.095

Splicing

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

Other links and lift over

dbSNP: rs11658127; hg19: chr17-66714282;