Variant 12-53971491-T-C details in Genebe, Genetics Data Aggregator

Variant summary

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

The NR_047517.2(HOTAIR):n.58-2735A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.514 in 152,204 control chromosomes in the GnomAD database, including 23,790 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 0.51 ( 23790 hom., cov: 34)

Consequence

HOTAIR
NR_047517.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.997

Variant links:

Genes affected

HOTAIR (HGNC:33510): (HOX transcript antisense RNA) This gene is located within the Homeobox C (HOXC) gene cluster on chromosome 12 and is co-expressed with the HOXC genes. It functions through an RNA product, which binds lysine specific demethylase 1 (LSD1) and Polycomb repressive complex 2 (PRC2), and serves as a scaffold to assemble these regulators at the HOXD gene cluster, thereby promoting epigenetic repression of HOXD. This gene is highly expressed in multiple tumors. Alternatively spliced transcript variants have been identified. [provided by RefSeq, Feb 2019]

HOTAIR links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.76).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.703 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect
HOTAIR	NR_047517.2 link	n.58-2735A>G	intron_variant
HOTAIR	NR_186240.1 link	n.181+1043A>G	intron_variant
HOTAIR	NR_186241.1 link	n.58-2735A>G	intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL
HOTAIR	ENST00000424518.5 link	n.60-2735A>G	intron_variant	5
HOTAIR	ENST00000455246.6 link	n.60-2735A>G	intron_variant	5
HOTAIR	ENST00000698798.1 link	n.481+1043A>G	intron_variant

Frequencies

GnomAD3 genomes

AF:

0.515

AC:

78336

AN:

152086

Hom.:

23800

Cov.:

show subpopulations

Gnomad AFR

AF:

0.169

Gnomad AMI

AF:

0.755

Gnomad AMR

AF:

0.576

Gnomad ASJ

AF:

0.540

Gnomad EAS

AF:

0.722

Gnomad SAS

AF:

0.584

Gnomad FIN

AF:

0.749

Gnomad MID

AF:

0.544

Gnomad NFE

AF:

0.649

Gnomad OTH

AF:

0.542

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

GnomAD4 genome

AF:

0.514

AC:

78308

AN:

152204

Hom.:

23790

Cov.:

AF XY:

0.523

AC XY:

38887

AN XY:

74412

show subpopulations

Gnomad4 AFR

AF:

0.169

Gnomad4 AMR

AF:

0.576

Gnomad4 ASJ

AF:

0.540

Gnomad4 EAS

AF:

0.722

Gnomad4 SAS

AF:

0.584

Gnomad4 FIN

AF:

0.749

Gnomad4 NFE

AF:

0.649

Gnomad4 OTH

AF:

0.535

Alfa

AF:

0.564

Hom.:

9494

Bravo

AF:

0.488

Asia WGS

AF:

0.601

AC:

2090

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.76

CADD

Benign

DANN

Benign

0.82

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