16-4874331-CTC-TTG

Variant names:

• chr16-4874331-CTC-TTG
• NM_001079514.3:c.1921_1923delCTCinsTTG
• UBN1 p.642

Variant summary

Our verdict is Likely benign. The variant received -1 ACMG points: 0P and 1B. BP7

The NM_001079514.3(UBN1):​c.1921_1923delCTCinsTTG​(p.642) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type MNV, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. L641L) has been classified as Benign.

• Frequency: Genomes: not found (cov: 33)
• Consequence: UBN1 NM_001079514.3 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.65
• Publications: 0 publications found

Genes affected

UBN1 (HGNC:12506): (ubinuclein 1) Cellular senescence is a hallmark of tumor suppression and tissue aging. Senescent cells contain domains of heterochromatin, called senescence-associated heterochromatin foci (SAHF), that repress proliferation-promoting genes. The protein encoded by this gene binds to proliferation-promoting genes and is required for SAHF formation, enhancing methylation of histone H3. [provided by RefSeq, Oct 2016]

ACMG classification

Our verdict: Likely_benign. The variant received -1 ACMG points.

• BP7: Synonymous conserved (PhyloP=2.65 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001079514.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UBN1	NM_001079514.3	MANE Select	c.1921_1923delCTCinsTTG	p.642	synonymous	N/A	NP_001072982.1	Q9NPG3-1
	UBN1	NM_001288656.1		c.1921_1923delCTCinsTTG	p.642	synonymous	N/A	NP_001275585.1	Q9NPG3-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UBN1	ENST00000262376.11	TSL:1 MANE Select	c.1921_1923delCTCinsTTG	p.642	synonymous	N/A	ENSP00000262376.5	Q9NPG3-1
	UBN1	ENST00000396658.8	TSL:1	c.1921_1923delCTCinsTTG	p.642	synonymous	N/A	ENSP00000379894.3	Q9NPG3-1
	UBN1	ENST00000931634.1		c.1894_1896delCTCinsTTG	p.633	synonymous	N/A	ENSP00000601693.1

Frequencies

GnomAD3 genomes Cov.: 33

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		2.6

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr16-4924332;