Genetic Variant LINC00851:n.202T>C (chr20-18380959-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000423033.1(LINC00851):n.202T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.84 in 455,986 control chromosomes in the GnomAD database, including 162,054 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 0.81 ( 50370 hom., cov: 33)

Exomes 𝑓: 0.86 ( 111684 hom. )

Consequence

LINC00851
ENST00000423033.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.37

Variant links:

Genes affected

LINC00851 (HGNC:43424): (long intergenic non-protein coding RNA 851)

LINC00851 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.94).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.863 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00851	NR_034167.1 link	n.202T>C		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00851	ENST00000423033.1 link	n.202T>C		non_coding_transcript_exon_variant	Exon 2 of 2	1
LINC00851	ENST00000594642.1 link	n.188T>C		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes

AF:

0.808

AC:

122920

AN:

152108

Hom.:

50354

Cov.:

show subpopulations

Gnomad AFR

AF:

0.658

Gnomad AMI

AF:

0.904

Gnomad AMR

AF:

0.834

Gnomad ASJ

AF:

0.859

Gnomad EAS

AF:

0.873

Gnomad SAS

AF:

0.836

Gnomad FIN

AF:

0.899

Gnomad MID

AF:

0.823

Gnomad NFE

AF:

0.869

Gnomad OTH

AF:

0.801

GnomAD3 exomes

AF:

0.851

AC:

109054

AN:

128122

Hom.:

46632

AF XY:

0.853

AC XY:

59820

AN XY:

70154

show subpopulations

Gnomad AFR exome

AF:

0.644

Gnomad AMR exome

AF:

0.855

Gnomad ASJ exome

AF:

0.854

Gnomad EAS exome

AF:

0.883

Gnomad SAS exome

AF:

0.840

Gnomad FIN exome

AF:

0.902

Gnomad NFE exome

AF:

0.868

Gnomad OTH exome

AF:

0.853

GnomAD4 exome

AF:

0.856

AC:

259982

AN:

303760

Hom.:

111684

Cov.:

AF XY:

0.856

AC XY:

148020

AN XY:

172982

show subpopulations

Gnomad4 AFR exome

AF:

0.653

Gnomad4 AMR exome

AF:

0.854

Gnomad4 ASJ exome

AF:

0.855

Gnomad4 EAS exome

AF:

0.879

Gnomad4 SAS exome

AF:

0.842

Gnomad4 FIN exome

AF:

0.899

Gnomad4 NFE exome

AF:

0.869

Gnomad4 OTH exome

AF:

0.847

GnomAD4 genome

AF:

0.808

AC:

122968

AN:

152226

Hom.:

50370

Cov.:

AF XY:

0.810

AC XY:

60293

AN XY:

74412

show subpopulations

Gnomad4 AFR

AF:

0.658

Gnomad4 AMR

AF:

0.834

Gnomad4 ASJ

AF:

0.859

Gnomad4 EAS

AF:

0.873

Gnomad4 SAS

AF:

0.837

Gnomad4 FIN

AF:

0.899

Gnomad4 NFE

AF:

0.869

Gnomad4 OTH

AF:

0.796

Alfa

AF:

0.852

Hom.:

72486

Bravo

AF:

0.793

Asia WGS

AF:

0.814

AC:

2831

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

0.70

DANN

Benign

0.26

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over