13-21140598-CGT-TTA

Variant names:

• chr13-21140598-CGT-TTA
• NM_005870.5:c.46_48delCGTinsTTA
• SAP18 p.Arg16Leu

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_005870.5(SAP18):​c.46_48delCGTinsTTA​(p.Arg16Leu) variant causes a missense 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. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R16H) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: SAP18 NM_005870.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.13
• Publications: 0 publications found

Genes affected

SAP18 (HGNC:10530): (Sin3A associated protein 18) Histone acetylation plays a key role in the regulation of eukaryotic gene expression. Histone acetylation and deacetylation are catalyzed by multisubunit complexes. The protein encoded by this gene is a component of the histone deacetylase complex, which includes SIN3, SAP30, HDAC1, HDAC2, RbAp46, RbAp48, and other polypeptides. This protein directly interacts with SIN3 and enhances SIN3-mediated transcriptional repression when tethered to the promoter. A pseudogene has been identified on chromosome 2. [provided by RefSeq, Dec 2008]

ENSG00000302602 (HGNC:):

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005870.5. 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
	SAP18	NM_005870.5	MANE Select	c.46_48delCGTinsTTA	p.Arg16Leu	missense	N/A	NP_005861.2	O00422-2
	SAP18	NM_001366643.2		c.-160_-158delCGTinsTTA		5_prime_UTR	Exon 1 of 5	NP_001353572.1
	SAP18	NR_172492.1		n.480_482delCGTinsTTA		non_coding_transcript_exon	Exon 1 of 3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SAP18	ENST00000382533.9	TSL:1 MANE Select	c.46_48delCGTinsTTA	p.Arg16Leu	missense	N/A	ENSP00000371973.4	O00422-2
	SAP18	ENST00000621421.4	TSL:1	c.46_48delCGTinsTTA	p.Arg16Leu	missense	N/A	ENSP00000481842.1	O00422-2
	SAP18	ENST00000607003.5	TSL:1	c.-12_-10delCGTinsTTA		5_prime_UTR	Exon 1 of 4	ENSP00000475925.1	O00422-1

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		1.1

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: chr13-21714737;