Variant rs619586 details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000619449.3(MALAT1):n.195A>G 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 0.0535 in 518,530 control chromosomes in the GnomAD database, including 1,238 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 0.036 ( 175 hom., cov: 32)

Exomes 𝑓: 0.061 ( 1063 hom. )

Consequence

MALAT1
ENST00000619449.3 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.183

Variant links:

Genes affected

MALAT1 (HGNC:29665): (metastasis associated lung adenocarcinoma transcript 1) This gene produces a precursor transcript from which a long non-coding RNA is derived by RNase P cleavage of a tRNA-like small ncRNA (known as mascRNA) from its 3' end. The resultant mature transcript lacks a canonical poly(A) tail but is instead stabilized by a 3' triple helical structure. This transcript is retained in the nucleus where it is thought to form molecular scaffolds for ribonucleoprotein complexes. It may act as a transcriptional regulator for numerous genes, including some genes involved in cancer metastasis and cell migration, and it is involved in cell cycle regulation. Its upregulation in multiple cancerous tissues has been associated with the proliferation and metastasis of tumor cells. [provided by RefSeq, Mar 2015]

MALAT1 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=-0.7).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.129 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MALAT1	NR_144567.1 link	n.961A>G		non_coding_transcript_exon_variant	1/2
MALAT1	NR_144568.1 link	n.961A>G		non_coding_transcript_exon_variant	1/3

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL
MALAT1	ENST00000534336.3 link	n.1059A>G	non_coding_transcript_exon_variant	1/1	6
MALAT1	ENST00000619449.3 link	n.195A>G	non_coding_transcript_exon_variant	2/3	3
MALAT1	ENST00000710855.1 link	n.311A>G	non_coding_transcript_exon_variant	1/2

Frequencies

GnomAD3 genomes

AF:

0.0356

AC:

5416

AN:

152082

Hom.:

177

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0119

Gnomad AMI

AF:

0.00658

Gnomad AMR

AF:

0.0535

Gnomad ASJ

AF:

0.0138

Gnomad EAS

AF:

0.0890

Gnomad SAS

AF:

0.138

Gnomad FIN

AF:

0.0376

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.0358

Gnomad OTH

AF:

0.0431

GnomAD3 exomes

AF:

0.0593

AC:

13726

AN:

231438

Hom.:

637

AF XY:

0.0615

AC XY:

7852

AN XY:

127680

show subpopulations

Gnomad AFR exome

AF:

0.0121

Gnomad AMR exome

AF:

0.0860

Gnomad ASJ exome

AF:

0.0142

Gnomad EAS exome

AF:

0.0841

Gnomad SAS exome

AF:

0.144

Gnomad FIN exome

AF:

0.0419

Gnomad NFE exome

AF:

0.0360

Gnomad OTH exome

AF:

0.0452

GnomAD4 exome

AF:

0.0610

AC:

22339

AN:

366330

Hom.:

1063

Cov.:

AF XY:

0.0662

AC XY:

13900

AN XY:

210066

show subpopulations

Gnomad4 AFR exome

AF:

0.0124

Gnomad4 AMR exome

AF:

0.0860

Gnomad4 ASJ exome

AF:

0.0164

Gnomad4 EAS exome

AF:

0.0824

Gnomad4 SAS exome

AF:

0.138

Gnomad4 FIN exome

AF:

0.0406

Gnomad4 NFE exome

AF:

0.0370

Gnomad4 OTH exome

AF:

0.0465

GnomAD4 genome

AF:

0.0355

AC:

5410

AN:

152200

Hom.:

175

Cov.:

AF XY:

0.0378

AC XY:

2810

AN XY:

74412

show subpopulations

Gnomad4 AFR

AF:

0.0118

Gnomad4 AMR

AF:

0.0534

Gnomad4 ASJ

AF:

0.0138

Gnomad4 EAS

AF:

0.0890

Gnomad4 SAS

AF:

0.138

Gnomad4 FIN

AF:

0.0376

Gnomad4 NFE

AF:

0.0358

Gnomad4 OTH

AF:

0.0427

Alfa

AF:

0.0384

Hom.:

213

Bravo

AF:

0.0345

Asia WGS

AF:

0.109

AC:

378

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.70

CADD

Benign

1.7

DANN

Benign

0.27

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