rs2366017

Variant names:

• chr17-69854760-G-A
• rs2366017
• ENST00000587241.1:n.307-47982G>A

Variant summary

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

The ENST00000587241.1(LINC01483):​n.307-47982G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0206 in 152,080 control chromosomes in the GnomAD database, including 47 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 0.021 (47 hom., cov: 32)
• Consequence: LINC01483 ENST00000587241.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0580
• Publications: 6 publications found

Genes affected

LINC01483 (HGNC:51130): (long intergenic non-protein coding RNA 1483)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0206 (3134/152080) while in subpopulation NFE AF = 0.0293 (1992/68000). AF 95% confidence interval is 0.0282. There are 47 homozygotes in GnomAd4. There are 1544 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 47 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000587241.1. 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
	LINC01483	NR_109971.1		n.363+9274G>A		intron	N/A
	LINC01483	NR_109972.1		n.363+9274G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01483	ENST00000587241.1	TSL:4	n.307-47982G>A		intron	N/A
	LINC01483	ENST00000588501.6	TSL:5	n.460+9274G>A		intron	N/A
	LINC01483	ENST00000591334.6	TSL:4	n.393+9274G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0206 AC: 3135 AN: 151962 Hom.: 47 Cov.: 32

Gnomad AFR AF: 0.00546

Gnomad AMI AF: 0.110

Gnomad AMR AF: 0.0251

Gnomad ASJ AF: 0.0283

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.00353

Gnomad FIN AF: 0.0247

Gnomad MID AF: 0.0191

Gnomad NFE AF: 0.0293

Gnomad OTH AF: 0.0245

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

GnomAD4 genome AF: 0.0206 AC: 3134 AN: 152080 Hom.: 47 Cov.: 32 AF XY: 0.0208 AC XY: 1544 AN XY: 74334

African (AFR) AF: 0.00545 AC: 226 AN: 41502

American (AMR) AF: 0.0250 AC: 382 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.0283 AC: 98 AN: 3468

East Asian (EAS) AF: 0.000194 AC: 1 AN: 5164

South Asian (SAS) AF: 0.00353 AC: 17 AN: 4818

European-Finnish (FIN) AF: 0.0247 AC: 261 AN: 10560

Middle Eastern (MID) AF: 0.0205 AC: 6 AN: 292

European-Non Finnish (NFE) AF: 0.0293 AC: 1992 AN: 68000

Other (OTH) AF: 0.0242 AC: 51 AN: 2106

Alfa AF: 0.0248 Hom.: 83

Bravo AF: 0.0209

Asia WGS AF: 0.00231 AC: 8 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.3
DANN	Benign	0.54
PhyloP100		-0.058
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs2366017; hg19: chr17-67850901;