1-46010775-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The ENST00000361297.7(MAST2):āc.1024A>Gā(p.Asn342Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000598 in 1,614,118 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. N342K) has been classified as Uncertain significance.
Frequency
Consequence
ENST00000361297.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MAST2 | NM_015112.3 | c.1024A>G | p.Asn342Asp | missense_variant | 10/29 | ENST00000361297.7 | NP_055927.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MAST2 | ENST00000361297.7 | c.1024A>G | p.Asn342Asp | missense_variant | 10/29 | 1 | NM_015112.3 | ENSP00000354671 | ||
MAST2 | ENST00000674079.1 | c.595A>G | p.Asn199Asp | missense_variant | 8/27 | ENSP00000501318 | P1 | |||
MAST2 | ENST00000372008.6 | c.679A>G | p.Asn227Asp | missense_variant | 8/20 | 5 | ENSP00000361078 | |||
MAST2 | ENST00000482881.1 | n.524A>G | non_coding_transcript_exon_variant | 6/6 | 3 |
Frequencies
GnomAD3 genomes AF: 0.000407 AC: 62AN: 152212Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000361 AC: 90AN: 249310Hom.: 0 AF XY: 0.000303 AC XY: 41AN XY: 135264
GnomAD4 exome AF: 0.000618 AC: 903AN: 1461788Hom.: 1 Cov.: 31 AF XY: 0.000597 AC XY: 434AN XY: 727198
GnomAD4 genome AF: 0.000407 AC: 62AN: 152330Hom.: 0 Cov.: 32 AF XY: 0.000349 AC XY: 26AN XY: 74478
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 16, 2021 | The c.1024A>G (p.N342D) alteration is located in exon 10 (coding exon 10) of the MAST2 gene. This alteration results from a A to G substitution at nucleotide position 1024, causing the asparagine (N) at amino acid position 342 to be replaced by an aspartic acid (D). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at