ENST00000597373.2:n.333-14701C>T

Variant names:

• chr16-86241478-G-A
• rs17245059
• ENST00000597373.2:n.333-14701C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000597373.2(LINC01081):​n.333-14701C>T variant causes a intron 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 ENST00000597373.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.998
• Publications: 2 publications found

Genes affected

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

LINC01082 (HGNC:49125): (long intergenic non-protein coding RNA 1082)

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LINC01081	NR_104139.1	n.395-14701C>T		intron_variant	Intron 3 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01081	ENST00000597373.2	n.333-14701C>T		intron_variant	Intron 3 of 5	5
LINC01081	ENST00000602425.2	n.465-14701C>T		intron_variant	Intron 3 of 7	2
LINC01081	ENST00000806422.1	n.480-14701C>T		intron_variant	Intron 4 of 6

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

African (AFR) AF: 0.102 AC: 4247 AN: 41486

American (AMR) AF: 0.203 AC: 3101 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.253 AC: 878 AN: 3470

East Asian (EAS) AF: 0.107 AC: 550 AN: 5162

South Asian (SAS) AF: 0.298 AC: 1437 AN: 4820

European-Finnish (FIN) AF: 0.208 AC: 2196 AN: 10574

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.196 AC: 13292 AN: 67964

Other (OTH) AF: 0.197 AC: 416 AN: 2108

Alfa AF: 0.194 Hom.: 4990

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
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs17245059; hg19: chr16-86275084;