Genetic Variant LINC00892:n.717C>T (chrX-136641425-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000427517.1(LINC00892):n.717C>T 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 0.281 in 109,972 control chromosomes in the GnomAD database, including 3,943 homozygotes. There are 8,822 hemizygotes in GnomAD. 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 0.28 ( 3942 hom., 8813 hem., cov: 21)

Exomes 𝑓: 0.27 ( 1 hom. 9 hem. )

Consequence

LINC00892
ENST00000427517.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.296

Variant links:

Genes affected

LINC00892 (HGNC:48578): (long intergenic non-protein coding RNA 892)

LINC00892 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=-0.96).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.459 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00892	NR_038461.1 link	n.362+552C>T		intron_variant	Intron 2 of 2
LINC00892	NR_038462.1 link	n.329+585C>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LINC00892	ENST00000427517.1 link	n.717C>T	non_coding_transcript_exon_variant	Exon 2 of 2	2
LINC00892	ENST00000656219.1 link	n.770C>T	non_coding_transcript_exon_variant	Exon 2 of 2
LINC00892	ENST00000429841.2 link	n.337+585C>T	intron_variant	Intron 2 of 2	2
LINC00892	ENST00000454385.8 link	n.366+552C>T	intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes

AF:

0.281

AC:

30834

AN:

109838

Hom.:

3939

Cov.:

AF XY:

0.273

AC XY:

8776

AN XY:

32132

show subpopulations

Gnomad AFR

AF:

0.466

Gnomad AMI

AF:

0.0553

Gnomad AMR

AF:

0.413

Gnomad ASJ

AF:

0.165

Gnomad EAS

AF:

0.0830

Gnomad SAS

AF:

0.330

Gnomad FIN

AF:

0.186

Gnomad MID

AF:

0.249

Gnomad NFE

AF:

0.180

Gnomad OTH

AF:

0.279

GnomAD4 exome

AF:

0.271

AC:

AN:

Hom.:

Cov.:

AF XY:

0.310

AC XY:

AN XY:

show subpopulations

Gnomad4 AFR exome

AF:

0.333

Gnomad4 EAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.196

Gnomad4 NFE exome

AF:

0.313

Gnomad4 OTH exome

AF:

1.00

GnomAD4 genome

AF:

0.281

AC:

30880

AN:

109887

Hom.:

3942

Cov.:

AF XY:

0.274

AC XY:

8813

AN XY:

32191

show subpopulations

Gnomad4 AFR

AF:

0.466

Gnomad4 AMR

AF:

0.414

Gnomad4 ASJ

AF:

0.165

Gnomad4 EAS

AF:

0.0833

Gnomad4 SAS

AF:

0.331

Gnomad4 FIN

AF:

0.186

Gnomad4 NFE

AF:

0.180

Gnomad4 OTH

AF:

0.284

Alfa

AF:

0.262

Hom.:

2605

Bravo

AF:

0.312

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

3.7

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