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

Variant summary

Our verdict is Benign. The variant received -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

Publications

3 publications found

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 was made for transcript

Our verdict: Benign. The variant received -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	ENST00000429841.3 link	n.337+585C>T	intron_variant	Intron 2 of 2	2

Frequencies

GnomAD3 genomes

AF:

0.281

AC:

30834

AN:

109838

Hom.:

3939

Cov.:

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

African (AFR)

AF:

0.333

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.196

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.313

AC:

AN:

Other (OTH)

AF:

1.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.513

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.281

AC:

30880

AN:

109887

Hom.:

3942

Cov.:

AF XY:

0.274

AC XY:

8813

AN XY:

32191

show subpopulations

African (AFR)

AF:

0.466

AC:

13994

AN:

30034

American (AMR)

AF:

0.414

AC:

4248

AN:

10266

Ashkenazi Jewish (ASJ)

AF:

0.165

AC:

434

AN:

2627

East Asian (EAS)

AF:

0.0833

AC:

293

AN:

3518

South Asian (SAS)

AF:

0.331

AC:

842

AN:

2547

European-Finnish (FIN)

AF:

0.186

AC:

1086

AN:

5854

Middle Eastern (MID)

AF:

0.263

AC:

AN:

213

European-Non Finnish (NFE)

AF:

0.180

AC:

9471

AN:

52667

Other (OTH)

AF:

0.284

AC:

418

AN:

1474

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

705

1409

2114

2818

3523

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

290

580

870

1160

1450

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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

(source)

DANN

Benign

0.26

PhyloP100

0.30

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over