16-86241478-G-C

Variant names:

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

Variant summary

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

The ENST00000602425.2(LINC01081):​n.465-14701C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.203 in 152,082 control chromosomes in the GnomAD database, including 3,750 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 0.20 (3750 hom., cov: 32)
• Consequence: LINC01081 ENST00000602425.2 intron
• 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=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.258 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01081	NR_104139.1	n.395-14701C>G		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>G		intron_variant	Intron 3 of 5	5
LINC01081	ENST00000602425.2	n.465-14701C>G		intron_variant	Intron 3 of 7	2

Frequencies

GnomAD3 genomes AF: 0.203 AC: 30801 AN: 151964 Hom.: 3746 Cov.: 32

Gnomad AFR AF: 0.0683

Gnomad AMI AF: 0.292

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.165

Gnomad EAS AF: 0.231

Gnomad SAS AF: 0.269

Gnomad FIN AF: 0.279

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.261

Gnomad OTH AF: 0.179

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

GnomAD4 genome AF: 0.203 AC: 30807 AN: 152082 Hom.: 3750 Cov.: 32 AF XY: 0.204 AC XY: 15199 AN XY: 74332

Gnomad4 AFR AF: 0.0682

Gnomad4 AMR AF: 0.231

Gnomad4 ASJ AF: 0.165

Gnomad4 EAS AF: 0.231

Gnomad4 SAS AF: 0.270

Gnomad4 FIN AF: 0.279

Gnomad4 NFE AF: 0.261

Gnomad4 OTH AF: 0.182

Alfa AF: 0.00641 Hom.: 4114

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.4
DANN	Benign	0.31

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;