3-183808051-GTG-CTT

Variant names:

• chr3-183808051-GTG-CTT
• NM_018023.5:c.4033_4035delGTGinsCTT
• YEATS2 p.Val1345Leu

Variant summary

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

The NM_018023.5(YEATS2):​c.4033_4035delGTGinsCTT​(p.Val1345Leu) variant causes a missense change. 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 nucleotide change resulting in the same amino acid substitution has been previously reported as Uncertain significance in ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V1345M) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: YEATS2 NM_018023.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 6.48
• Publications: 0 publications found

Genes affected

YEATS2 (HGNC:25489): (YEATS domain containing 2) Summary: The protein encoded by this gene is a scaffolding subunit of the ATAC complex, which is a complex with acetyltransferase activity on histones H3 and H4. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, May 2017]

YEATS2-AS1 (HGNC:41101): (YEATS2 antisense RNA 1)

ACMG classification

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018023.5. 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
	YEATS2	NM_018023.5	MANE Select	c.4033_4035delGTGinsCTT	p.Val1345Leu	missense	N/A	NP_060493.3
	YEATS2	NM_001351370.2		c.4036_4038delGTGinsCTT	p.Val1346Leu	missense	N/A	NP_001338299.1
	YEATS2	NM_001351369.2		c.4033_4035delGTGinsCTT	p.Val1345Leu	missense	N/A	NP_001338298.1	Q9ULM3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	YEATS2	ENST00000305135.10	TSL:1 MANE Select	c.4033_4035delGTGinsCTT	p.Val1345Leu	missense	N/A	ENSP00000306983.5	Q9ULM3
	YEATS2	ENST00000884732.1		c.4036_4038delGTGinsCTT	p.Val1346Leu	missense	N/A	ENSP00000554791.1
	YEATS2	ENST00000884736.1		c.4036_4038delGTGinsCTT	p.Val1346Leu	missense	N/A	ENSP00000554795.1

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		6.5

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: chr3-183525839;