rs4843359

Positions:

• chr16-86243835-G-A
• chr16-86243835-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.395-17058C>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 0.0733 in 152,300 control chromosomes in the GnomAD database, including 987 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 0.073 (987 hom., cov: 33)
• Consequence: LINC01081 NR_104139.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13

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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.444 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01081	NR_104139.1	n.395-17058C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01081	ENST00000597373.2	n.333-17058C>T		intron_variant, non_coding_transcript_variant		5
LINC01081	ENST00000602425.2	n.465-17058C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0731 AC: 11131 AN: 152182 Hom.: 983 Cov.: 33

Gnomad AFR AF: 0.0467

Gnomad AMI AF: 0.0537

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.0605

Gnomad EAS AF: 0.459

Gnomad SAS AF: 0.113

Gnomad FIN AF: 0.0786

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0360

Gnomad OTH AF: 0.0793

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

GnomAD4 genome AF: 0.0733 AC: 11160 AN: 152300 Hom.: 987 Cov.: 33 AF XY: 0.0804 AC XY: 5990 AN XY: 74462

Gnomad4 AFR AF: 0.0469

Gnomad4 AMR AF: 0.167

Gnomad4 ASJ AF: 0.0605

Gnomad4 EAS AF: 0.459

Gnomad4 SAS AF: 0.112

Gnomad4 FIN AF: 0.0786

Gnomad4 NFE AF: 0.0360

Gnomad4 OTH AF: 0.0814

Alfa AF: 0.0401 Hom.: 166

Bravo AF: 0.0829

Asia WGS AF: 0.258 AC: 893 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.58
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4843359; hg19: chr16-86277441;