rs664589
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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
NR_002819.4 non_coding_transcript_exon
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.285
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]
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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 | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MALAT1 | NR_002819.4 | n.4141C>G | non_coding_transcript_exon_variant | 1/1 | |||
TALAM1 | NR_145459.1 | n.5555G>C | non_coding_transcript_exon_variant | 1/1 | |||
MALAT1 | NR_144567.1 | n.3907C>G | non_coding_transcript_exon_variant | 2/2 | |||
MALAT1 | NR_144568.1 | 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 | n.4239C>G | non_coding_transcript_exon_variant | 1/1 | |||||
TALAM1 | ENST00000698129.1 | n.5555G>C | non_coding_transcript_exon_variant | 1/1 |
Frequencies
GnomAD3 genomes ? AF: 0.0396 AC: 6017AN: 152012Hom.: 186 Cov.: 32
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GnomAD3 exomes AF: 0.0601 AC: 13702AN: 228018Hom.: 616 AF XY: 0.0624 AC XY: 7844AN XY: 125804
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GnomAD4 exome AF: 0.0617 AC: 22502AN: 364868Hom.: 1062 Cov.: 0 AF XY: 0.0667 AC XY: 13962AN XY: 209174
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GnomAD4 genome ? AF: 0.0396 AC: 6021AN: 152130Hom.: 185 Cov.: 32 AF XY: 0.0415 AC XY: 3087AN XY: 74362
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at