rs16974356

chr17-69762865-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_109971.1(LINC01483):n.317-82575C>T 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 0.119 in 152,098 control chromosomes in the GnomAD database, including 1,583 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 (1583 hom., cov: 32)
• Consequence: LINC01483 NR_109971.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.272

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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.353 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01483	NR_109971.1	n.317-82575C>T		intron_variant, non_coding_transcript_variant
LINC01483	NR_109972.1	n.317-82575C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01483	ENST00000591334.5	n.317-82575C>T		intron_variant, non_coding_transcript_variant		4
LINC01483	ENST00000588185.1	n.159-82575C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.119 AC: 18149 AN: 151980 Hom.: 1580 Cov.: 32

Gnomad AFR AF: 0.0302

Gnomad AMI AF: 0.0440

Gnomad AMR AF: 0.177

Gnomad ASJ AF: 0.125

Gnomad EAS AF: 0.366

Gnomad SAS AF: 0.273

Gnomad FIN AF: 0.180

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.119 AC: 18159 AN: 152098 Hom.: 1583 Cov.: 32 AF XY: 0.128 AC XY: 9493 AN XY: 74326

Gnomad4 AFR AF: 0.0302

Gnomad4 AMR AF: 0.177

Gnomad4 ASJ AF: 0.125

Gnomad4 EAS AF: 0.367

Gnomad4 SAS AF: 0.273

Gnomad4 FIN AF: 0.180

Gnomad4 NFE AF: 0.122

Gnomad4 OTH AF: 0.119

Alfa AF: 0.124 Hom.: 239

Bravo AF: 0.114

Asia WGS AF: 0.289 AC: 1001 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	3.9
Dann	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16974356; hg19: chr17-67759006;