rs2366017

chr17-69854760-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NR_109971.1(LINC01483):n.363+9274G>A variant causes a intron, non coding transcript 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 NR_109971.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0580

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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 male gnomad4 subpopulation. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 47 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01483	NR_109971.1	n.363+9274G>A		intron_variant, non_coding_transcript_variant
LINC01483	NR_109972.1	n.363+9274G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01483	ENST00000591334.5	n.363+9274G>A		intron_variant, non_coding_transcript_variant		4
LINC01483	ENST00000587241.1	n.307-47982G>A		intron_variant, non_coding_transcript_variant		4
LINC01483	ENST00000659331.1	n.199+9274G>A		intron_variant, non_coding_transcript_variant
LINC01483	ENST00000665875.1	n.176+9274G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.00545

Gnomad4 AMR AF: 0.0250

Gnomad4 ASJ AF: 0.0283

Gnomad4 EAS AF: 0.000194

Gnomad4 SAS AF: 0.00353

Gnomad4 FIN AF: 0.0247

Gnomad4 NFE AF: 0.0293

Gnomad4 OTH AF: 0.0242

Alfa AF: 0.0243 Hom.: 7

Bravo AF: 0.0209

Asia WGS AF: 0.00231 AC: 8 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	4.3
Dann	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2366017; hg19: chr17-67850901;