17-68629653-C-T

Position:

• chr17-68629653-C-T

Variant summary

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

The NR_110825.1(LINC01482):​n.33+1467C>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 0.0248 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 NR_110825.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.450

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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 male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 57 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01482	NR_110825.1	n.33+1467C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01482	ENST00000585484.1	n.33+1467C>T		intron_variant, non_coding_transcript_variant		1
LINC01482	ENST00000587999.1	n.198+31507C>T		intron_variant, non_coding_transcript_variant		3
LINC01482	ENST00000589610.5	n.41-28995C>T		intron_variant, non_coding_transcript_variant		3
LINC01482	ENST00000591754.1	n.84+1467C>T		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.00616

Gnomad4 AMR AF: 0.0155

Gnomad4 ASJ AF: 0.0325

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.00767

Gnomad4 FIN AF: 0.0566

Gnomad4 NFE AF: 0.0361

Gnomad4 OTH AF: 0.0289

Alfa AF: 0.0334 Hom.: 28

Bravo AF: 0.0213

Asia WGS AF: 0.00144 AC: 5 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs77325336; hg19: chr17-66625794;