rs17245059

chr16-86241478-G-Achr16-86241478-G-C

Variant summary

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

The NR_104139.1(LINC01081):n.395-14701C>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 0.174 in 152,068 control chromosomes in the GnomAD database, including 2,554 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 0.17 (2554 hom., cov: 32)
• Consequence: LINC01081 NR_104139.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.998

Genes affected

LINC01081 (HGNC:49124): (long intergenic non-protein coding RNA 1081)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.285 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01081	NR_104139.1	n.395-14701C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01081	ENST00000597373.2	n.333-14701C>T		intron_variant, non_coding_transcript_variant		5
LINC01081	ENST00000602425.2	n.465-14701C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.174 AC: 26424 AN: 151950 Hom.: 2550 Cov.: 32

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.239

Gnomad AMR AF: 0.202

Gnomad ASJ AF: 0.253

Gnomad EAS AF: 0.106

Gnomad SAS AF: 0.298

Gnomad FIN AF: 0.208

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.196

Gnomad OTH AF: 0.199

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

GnomAD4 genome AF: 0.174 AC: 26430 AN: 152068 Hom.: 2554 Cov.: 32 AF XY: 0.178 AC XY: 13220 AN XY: 74330

Gnomad4 AFR AF: 0.102

Gnomad4 AMR AF: 0.203

Gnomad4 ASJ AF: 0.253

Gnomad4 EAS AF: 0.107

Gnomad4 SAS AF: 0.298

Gnomad4 FIN AF: 0.208

Gnomad4 NFE AF: 0.196

Gnomad4 OTH AF: 0.197

Alfa AF: 0.199 Hom.: 4114

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	4.3
Dann	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17245059; hg19: chr16-86275084;