17-68629653-C-T

Variant names:

• chr17-68629653-C-T
• rs77325336
• ENST00000585484.1:n.33+1467C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000585484.1(LINC01482):​n.33+1467C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0248 in 152,254 control chromosomes in the GnomAD database, including 57 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 0.025 (57 hom., cov: 33)
• Consequence: LINC01482 ENST00000585484.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.450
• Publications: 2 publications found

Genes affected

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

ENSG00000303223 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0248 (3775/152254) while in subpopulation NFE AF = 0.0361 (2454/68012). AF 95% confidence interval is 0.0349. There are 57 homozygotes in GnomAd4. There are 1883 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 57 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000585484.1. 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
	LINC01482	NR_110825.1		n.33+1467C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01482	ENST00000585484.1	TSL:1	n.33+1467C>T		intron	N/A
	LINC01482	ENST00000587999.1	TSL:3	n.198+31507C>T		intron	N/A
	LINC01482	ENST00000589610.5	TSL:3	n.41-28995C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0248 AC: 3778 AN: 152136 Hom.: 57 Cov.: 33

Gnomad AFR AF: 0.00618

Gnomad AMI AF: 0.0164

Gnomad AMR AF: 0.0156

Gnomad ASJ AF: 0.0325

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.00787

Gnomad FIN AF: 0.0566

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0361

Gnomad OTH AF: 0.0292

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

GnomAD4 genome AF: 0.0248 AC: 3775 AN: 152254 Hom.: 57 Cov.: 33 AF XY: 0.0253 AC XY: 1883 AN XY: 74456

African (AFR) AF: 0.00616 AC: 256 AN: 41546

American (AMR) AF: 0.0155 AC: 237 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0325 AC: 113 AN: 3472

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5186

South Asian (SAS) AF: 0.00767 AC: 37 AN: 4822

European-Finnish (FIN) AF: 0.0566 AC: 600 AN: 10604

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.0361 AC: 2454 AN: 68012

Other (OTH) AF: 0.0289 AC: 61 AN: 2114

Alfa AF: 0.0336 Hom.: 159

Bravo AF: 0.0213

Asia WGS AF: 0.00144 AC: 5 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.2
DANN	Benign	0.72
PhyloP100		0.45

Splicing

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

Other links and lift over

dbSNP: rs77325336; hg19: chr17-66625794;