10-27155311-CG-C

Variant names:

• chr10-27155311-CG-C
• rs150868633
• ENST00000375946.8:c.-112delG

Variant summary

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

The ENST00000375946.8(MASTL):​c.-112delG variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000114 in 878,150 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 31)
  • Exomes 𝑓: 0.0000011 (0 hom.)
• Consequence: MASTL ENST00000375946.8 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.51

Genes affected

MASTL (HGNC:19042): (microtubule associated serine/threonine kinase like) This gene encodes a microtubule-associated serine/threonine kinase. Mutations at this locus have been associated with autosomal dominant thrombocytopenia, also known as thrombocytopenia-2. Alternatively spliced transcript variants have been described for this locus. [provided by RefSeq, Feb 2010]

YME1L1 (HGNC:12843): (YME1 like 1 ATPase) The protein encoded by this gene is the human ortholog of yeast mitochondrial AAA metalloprotease, Yme1p. It is localized in the mitochondria and can functionally complement a yme1 disruptant yeast strain. It is proposed that this gene plays a role in mitochondrial protein metabolism and could be involved in mitochondrial pathologies. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2011]

ACMG classification

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MASTL	NM_001172303.3	c.-115delG		upstream_gene_variant		ENST00000375940.9	NP_001165774.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MASTL	ENST00000375946.8	c.-112delG		5_prime_UTR_variant	Exon 1 of 12	1		ENSP00000365113.4
MASTL	ENST00000375940.9	c.-115delG		upstream_gene_variant		1	NM_001172303.3	ENSP00000365107.5
YME1L1	ENST00000477432.1	c.-1102delC		upstream_gene_variant		1		ENSP00000473302.1
MASTL	ENST00000342386.10	c.-115delG		upstream_gene_variant		2		ENSP00000343446.5

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome AF: 0.00000114 AC: 1 AN: 878150 Hom.: 0 Cov.: 12 AF XY: 0.00000227 AC XY: 1 AN XY: 441438

African (AFR) AF: 0.00 AC: 0 AN: 20402

American (AMR) AF: 0.00 AC: 0 AN: 23192

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 16952

East Asian (EAS) AF: 0.00 AC: 0 AN: 32890

South Asian (SAS) AF: 0.0000175 AC: 1 AN: 57068

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 31474

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2830

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 653330

Other (OTH) AF: 0.00 AC: 0 AN: 40012

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		2.5

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

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Other links and lift over

dbSNP: rs150868633; hg19: chr10-27444240;