chr19-48714849-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001130915.2(MAMSTR):c.485C>G(p.Pro162Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000683 in 1,611,182 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000026 ( 0 hom., cov: 30)
Exomes 𝑓: 0.0000048 ( 0 hom. )
Consequence
MAMSTR
NM_001130915.2 missense
NM_001130915.2 missense
Scores
3
16
Clinical Significance
Conservation
PhyloP100: 3.30
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]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MAMSTR | NM_001130915.2 | c.485C>G | p.Pro162Arg | missense_variant | 6/10 | ENST00000318083.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAMSTR | ENST00000318083.11 | c.485C>G | p.Pro162Arg | missense_variant | 6/10 | 2 | NM_001130915.2 | P2 | |
MAMSTR | ENST00000594582.1 | c.176C>G | p.Pro59Arg | missense_variant | 4/7 | 1 | |||
MAMSTR | ENST00000356751.8 | c.176C>G | p.Pro59Arg | missense_variant | 4/8 | 2 | A2 | ||
MAMSTR | ENST00000599703.1 | c.635C>G | p.Pro212Arg | missense_variant | 6/6 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000264 AC: 4AN: 151696Hom.: 0 Cov.: 30
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GnomAD3 exomes AF: 0.00000813 AC: 2AN: 245892Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 133342
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GnomAD4 exome AF: 0.00000480 AC: 7AN: 1459372Hom.: 0 Cov.: 33 AF XY: 0.00000413 AC XY: 3AN XY: 726066
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GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 151810Hom.: 0 Cov.: 30 AF XY: 0.0000135 AC XY: 1AN XY: 74190
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 18, 2022 | The c.485C>G (p.P162R) alteration is located in exon 6 (coding exon 5) of the MAMSTR gene. This alteration results from a C to G substitution at nucleotide position 485, causing the proline (P) at amino acid position 162 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Pathogenic
Dann
Uncertain
DEOGEN2
Benign
T;.;.;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
D
LIST_S2
Benign
T;T;T;T
M_CAP
Benign
T
MetaRNN
Benign
T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
L;.;.;.
MutationTaster
Benign
N;N;N;N
PrimateAI
Benign
T
PROVEAN
Benign
N;D;.;.
REVEL
Benign
Sift
Uncertain
D;D;.;.
Sift4G
Uncertain
D;D;D;.
Polyphen
P;.;.;.
Vest4
MutPred
Loss of glycosylation at P162 (P = 0.0069);.;.;.;
MVP
MPC
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
DS_AG_spliceai
Position offset: 24
Find out detailed SpliceAI scores and Pangolin per-transcript scores at