ENST00000850956.1:n.2834C>T

Variant names:

• chr11-65501878-C-T
• rs664589
• ENST00000850956.1:n.2834C>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.285
• Publications: 41 publications found

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)

ACMG classification

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).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000850956.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MALAT1	NR_002819.5	MANE Select	n.2834C>T		non_coding_transcript_exon	Exon 1 of 1
	MALAT1	NR_144567.1		n.3907C>T		non_coding_transcript_exon	Exon 2 of 2
	MALAT1	NR_144568.1		n.3907C>T		non_coding_transcript_exon	Exon 2 of 3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MALAT1	ENST00000850956.1	MANE Select	n.2834C>T		non_coding_transcript_exon	Exon 1 of 1
	MALAT1	ENST00000508832.3	TSL:2	n.2837C>T		non_coding_transcript_exon	Exon 1 of 2
	MALAT1	ENST00000534336.4	TSL:6	n.4273C>T		non_coding_transcript_exon	Exon 1 of 1

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 v4.9

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

Other links and lift over

dbSNP: rs664589; hg19: chr11-65269349;