Variant rs7927113 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.2990G>A 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 0.0147 in 518,992 control chromosomes in the GnomAD database, including 406 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 0.035 ( 295 hom., cov: 32)

Exomes 𝑓: 0.0060 ( 111 hom. )

Consequence

MALAT1
NR_002819.4 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.556

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=-0.74).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.118 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons
MALAT1	NR_002819.4 linkuse as main transcript	n.2990G>A	non_coding_transcript_exon_variant	1/1
TALAM1	NR_145459.1 linkuse as main transcript	n.6706C>T	non_coding_transcript_exon_variant	1/1
MALAT1	NR_144567.1 linkuse as main transcript	n.2756G>A	non_coding_transcript_exon_variant	2/2
MALAT1	NR_144568.1 linkuse as main transcript	n.2756G>A	non_coding_transcript_exon_variant	2/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MALAT1	ENST00000534336.3 linkuse as main transcript	n.3088G>A		non_coding_transcript_exon_variant	1/1
TALAM1	ENST00000698129.1 linkuse as main transcript	n.6706C>T		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes

AF:

0.0354

AC:

5390

AN:

152158

Hom.:

294

Cov.:

show subpopulations

Gnomad AFR

AF:

0.120

Gnomad AMI

AF:

0.00658

Gnomad AMR

AF:

0.0148

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00692

Gnomad SAS

AF:

0.00228

Gnomad FIN

AF:

0.000282

Gnomad MID

AF:

0.0222

Gnomad NFE

AF:

0.000941

Gnomad OTH

AF:

0.0240

GnomAD3 exomes

AF:

0.00992

AC:

2300

AN:

231870

Hom.:

124

AF XY:

0.00807

AC XY:

1032

AN XY:

127896

show subpopulations

Gnomad AFR exome

AF:

0.126

Gnomad AMR exome

AF:

0.00632

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00580

Gnomad SAS exome

AF:

0.00294

Gnomad FIN exome

AF:

0.000515

Gnomad NFE exome

AF:

0.000822

Gnomad OTH exome

AF:

0.00613

GnomAD4 exome

AF:

0.00600

AC:

2202

AN:

366716

Hom.:

111

Cov.:

AF XY:

0.00494

AC XY:

1039

AN XY:

210268

show subpopulations

Gnomad4 AFR exome

AF:

0.130

Gnomad4 AMR exome

AF:

0.00606

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00721

Gnomad4 SAS exome

AF:

0.00313

Gnomad4 FIN exome

AF:

0.000532

Gnomad4 NFE exome

AF:

0.000672

Gnomad4 OTH exome

AF:

0.00969

GnomAD4 genome

AF:

0.0355

AC:

5402

AN:

152276

Hom.:

295

Cov.:

AF XY:

0.0350

AC XY:

2606

AN XY:

74468

show subpopulations

Gnomad4 AFR

AF:

0.120

Gnomad4 AMR

AF:

0.0148

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00693

Gnomad4 SAS

AF:

0.00228

Gnomad4 FIN

AF:

0.000282

Gnomad4 NFE

AF:

0.000941

Gnomad4 OTH

AF:

0.0237

Alfa

AF:

0.0154

Hom.:

Bravo

AF:

0.0411

Asia WGS

AF:

0.0170

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.74

CADD

Benign

DANN

Benign

0.84

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