NM_001393504.1:c.2690G>A

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_001393504.1(MAST3):​c.2690G>A​(p.Gly897Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000274 in 1,457,616 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. 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. G897V) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 33)
Exomes 𝑓: 0.0000027 ( 0 hom. )

Consequence

MAST3
NM_001393504.1 missense

Scores

1
18

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.683
Variant links:
Genes affected
MAST3 (HGNC:19036): (microtubule associated serine/threonine kinase 3) Predicted to enable protein serine/threonine kinase activity. Predicted to be involved in cytoskeleton organization; intracellular signal transduction; and peptidyl-serine phosphorylation. [provided by Alliance of Genome Resources, Apr 2022]
MAST3-AS1 (HGNC:55276): (MAST3 antisense RNA 1)

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.0671995).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
MAST3NM_001393504.1 linkc.2690G>A p.Gly897Asp missense_variant Exon 23 of 28 ENST00000687212.1 NP_001380433.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
MAST3ENST00000687212.1 linkc.2690G>A p.Gly897Asp missense_variant Exon 23 of 28 NM_001393504.1 ENSP00000509890.1 A0A8I5KST9

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
AF:
0.00000274
AC:
4
AN:
1457616
Hom.:
0
Cov.:
36
AF XY:
0.00000276
AC XY:
2
AN XY:
725240
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000270
Gnomad4 OTH exome
AF:
0.0000166
GnomAD4 genome
Cov.:
33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.26
BayesDel_addAF
Benign
-0.13
T
BayesDel_noAF
Benign
-0.42
CADD
Benign
17
DANN
Benign
0.97
DEOGEN2
Benign
0.012
T
Eigen
Benign
-0.73
Eigen_PC
Benign
-0.74
FATHMM_MKL
Benign
0.088
N
LIST_S2
Benign
0.72
T
M_CAP
Benign
0.026
D
MetaRNN
Benign
0.067
T
MetaSVM
Benign
-0.91
T
MutationAssessor
Benign
1.1
L
PrimateAI
Uncertain
0.49
T
PROVEAN
Benign
-0.24
N
REVEL
Benign
0.077
Sift
Benign
0.033
D
Sift4G
Benign
0.44
T
Polyphen
0.11
B
Vest4
0.16
MutPred
0.30
Gain of relative solvent accessibility (P = 0.0082);
MVP
0.37
MPC
1.0
ClinPred
0.14
T
GERP RS
1.7
Varity_R
0.066
gMVP
0.36

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr19-18255381; COSMIC: COSV53224796; COSMIC: COSV53224796; API