GeneBe

11-65501878-C-T

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The ENST00000850956.1(MALAT1):​n.2834C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

MALAT1
ENST00000850956.1 non_coding_transcript_exon

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.285

Publications

41 publications found
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]
TALAM1 (HGNC:54476): (TALAM1 transcript, MALAT1 antisense RNA)

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.53).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
MALAT1NR_002819.5 linkn.2834C>T non_coding_transcript_exon_variant Exon 1 of 1 ENST00000850956.1
MALAT1NR_144567.1 linkn.3907C>T non_coding_transcript_exon_variant Exon 2 of 2
MALAT1NR_144568.1 linkn.3907C>T non_coding_transcript_exon_variant Exon 2 of 3
TALAM1NR_145459.1 linkn.5555G>A non_coding_transcript_exon_variant Exon 1 of 1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
MALAT1ENST00000850956.1 linkn.2834C>T non_coding_transcript_exon_variant Exon 1 of 1 NR_002819.5

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
364938
Hom.:
0
Cov.:
0
AF XY:
0.00
AC XY:
0
AN XY:
209228
African (AFR)
AF:
0.00
AC:
0
AN:
10496
American (AMR)
AF:
0.00
AC:
0
AN:
35806
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
11694
East Asian (EAS)
AF:
0.00
AC:
0
AN:
13154
South Asian (SAS)
AF:
0.00
AC:
0
AN:
66592
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
16870
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
2852
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
190930
Other (OTH)
AF:
0.00
AC:
0
AN:
16544
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.53
CADD
Benign
12
DANN
Benign
0.79
PhyloP100
-0.28

Splicing

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

Publications

Other links and lift over

dbSNP: rs664589; hg19: chr11-65269349; API