17-68689706-C-T

Position:

• chr17-68689706-C-T

Variant summary

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

The ENST00000587999.1(LINC01482):​n.199-73784C>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 0.0937 in 152,252 control chromosomes in the GnomAD database, including 877 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 0.094 (877 hom., cov: 33)
• Consequence: LINC01482 ENST00000587999.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.576

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.166 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01482	ENST00000587999.1	n.199-73784C>T		intron_variant, non_coding_transcript_variant		3
LINC01482	ENST00000589610.5	n.128+30971C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0936 AC: 14246 AN: 152134 Hom.: 874 Cov.: 33

Gnomad AFR AF: 0.169

Gnomad AMI AF: 0.0417

Gnomad AMR AF: 0.0459

Gnomad ASJ AF: 0.0862

Gnomad EAS AF: 0.00404

Gnomad SAS AF: 0.149

Gnomad FIN AF: 0.0870

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0639

Gnomad OTH AF: 0.0831

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

GnomAD4 genome AF: 0.0937 AC: 14260 AN: 152252 Hom.: 877 Cov.: 33 AF XY: 0.0942 AC XY: 7013 AN XY: 74446

Gnomad4 AFR AF: 0.169

Gnomad4 AMR AF: 0.0458

Gnomad4 ASJ AF: 0.0862

Gnomad4 EAS AF: 0.00405

Gnomad4 SAS AF: 0.148

Gnomad4 FIN AF: 0.0870

Gnomad4 NFE AF: 0.0638

Gnomad4 OTH AF: 0.0841

Alfa AF: 0.0790 Hom.: 100

Bravo AF: 0.0923

Asia WGS AF: 0.0930 AC: 323 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.1
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7213314; hg19: chr17-66685847;