Variant 11-65501878-C-G details in Genebe, Genetics Data Aggregator

Variant summary

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

The NR_002819.4(MALAT1):n.4141C>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 0.0552 in 516,998 control chromosomes in the GnomAD database, including 1,247 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 0.040 ( 185 hom., cov: 32)

Exomes 𝑓: 0.062 ( 1062 hom. )

Consequence

MALAT1
NR_002819.4 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.285

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:

TALAM1 (HGNC:54476): (TALAM1 transcript, MALAT1 antisense RNA)

TALAM1 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=-0.55).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.13 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons
MALAT1	NR_002819.4 linkuse as main transcript	n.4141C>G	non_coding_transcript_exon_variant	1/1
TALAM1	NR_145459.1 linkuse as main transcript	n.5555G>C	non_coding_transcript_exon_variant	1/1
MALAT1	NR_144567.1 linkuse as main transcript	n.3907C>G	non_coding_transcript_exon_variant	2/2
MALAT1	NR_144568.1 linkuse as main transcript	n.3907C>G	non_coding_transcript_exon_variant	2/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MALAT1	ENST00000534336.3 linkuse as main transcript	n.4239C>G		non_coding_transcript_exon_variant	1/1
TALAM1	ENST00000698129.1 linkuse as main transcript	n.5555G>C		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes

AF:

0.0396

AC:

6017

AN:

152012

Hom.:

186

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0238

Gnomad AMI

AF:

0.00658

Gnomad AMR

AF:

0.0551

Gnomad ASJ

AF:

0.0136

Gnomad EAS

AF:

0.0824

Gnomad SAS

AF:

0.139

Gnomad FIN

AF:

0.0373

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.0375

Gnomad OTH

AF:

0.0469

GnomAD3 exomes

AF:

0.0601

AC:

13702

AN:

228018

Hom.:

616

AF XY:

0.0624

AC XY:

7844

AN XY:

125804

show subpopulations

Gnomad AFR exome

AF:

0.0236

Gnomad AMR exome

AF:

0.0858

Gnomad ASJ exome

AF:

0.0142

Gnomad EAS exome

AF:

0.0790

Gnomad SAS exome

AF:

0.143

Gnomad FIN exome

AF:

0.0416

Gnomad NFE exome

AF:

0.0371

Gnomad OTH exome

AF:

0.0469

GnomAD4 exome

AF:

0.0617

AC:

22502

AN:

364868

Hom.:

1062

Cov.:

AF XY:

0.0667

AC XY:

13962

AN XY:

209174

show subpopulations

Gnomad4 AFR exome

AF:

0.0251

Gnomad4 AMR exome

AF:

0.0860

Gnomad4 ASJ exome

AF:

0.0162

Gnomad4 EAS exome

AF:

0.0777

Gnomad4 SAS exome

AF:

0.137

Gnomad4 FIN exome

AF:

0.0405

Gnomad4 NFE exome

AF:

0.0382

Gnomad4 OTH exome

AF:

0.0465

GnomAD4 genome

AF:

0.0396

AC:

6021

AN:

152130

Hom.:

185

Cov.:

AF XY:

0.0415

AC XY:

3087

AN XY:

74362

show subpopulations

Gnomad4 AFR

AF:

0.0240

Gnomad4 AMR

AF:

0.0549

Gnomad4 ASJ

AF:

0.0136

Gnomad4 EAS

AF:

0.0826

Gnomad4 SAS

AF:

0.138

Gnomad4 FIN

AF:

0.0373

Gnomad4 NFE

AF:

0.0375

Gnomad4 OTH

AF:

0.0464

Alfa

AF:

0.0331

Hom.:

Bravo

AF:

0.0389

Asia WGS

AF:

0.0950

AC:

329

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.55

CADD

Benign

DANN

Benign

0.82

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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