19-48713540-GGG-CGA

Variant names:

• chr19-48713540-GGG-CGA
• NM_001130915.2:c.973_975delCCCinsTCG
• MAMSTR p.Pro325Ser

Variant summary

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

The NM_001130915.2(MAMSTR):​c.973_975delCCCinsTCG​(p.Pro325Ser) 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.

• Frequency: Genomes: not found (cov: 32)
• Consequence: MAMSTR NM_001130915.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.99
• Publications: 0 publications found

Genes affected

MAMSTR (HGNC:26689): (MEF2 activating motif and SAP domain containing transcriptional regulator) Predicted to enable transcription coregulator activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to act upstream of or within positive regulation of myotube differentiation and positive regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001130915.2. 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
	MAMSTR	NM_001130915.2	MANE Select	c.973_975delCCCinsTCG	p.Pro325Ser	missense	N/A	NP_001124387.1	Q6ZN01-1
	MAMSTR	NM_182574.3		c.664_666delCCCinsTCG	p.Pro222Ser	missense	N/A	NP_872380.1	Q6ZN01-2
	MAMSTR	NM_001297753.2		c.469_471delCCCinsTCG	p.Pro157Ser	missense	N/A	NP_001284682.1	Q6ZN01-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAMSTR	ENST00000318083.11	TSL:2 MANE Select	c.973_975delCCCinsTCG	p.Pro325Ser	missense	N/A	ENSP00000324175.5	Q6ZN01-1
	MAMSTR	ENST00000594582.1	TSL:1	c.469_471delCCCinsTCG	p.Pro157Ser	missense	N/A	ENSP00000471590.1	Q6ZN01-3
	MAMSTR	ENST00000599703.2	TSL:5	c.1123_1125delCCCinsTCG	p.Pro375Ser	missense	N/A	ENSP00000469544.2	M0QY28

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		5.0

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: chr19-49216797;