1-45824425-C-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_015112.3(MAST2):c.178-8C>G variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00119 in 1,582,822 control chromosomes in the GnomAD database, including 27 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_015112.3 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MAST2 | NM_015112.3 | c.178-8C>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000361297.7 | NP_055927.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MAST2 | ENST00000361297.7 | c.178-8C>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_015112.3 | ENSP00000354671 | ||||
MAST2 | ENST00000470809.1 | n.147-8C>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.00657 AC: 1000AN: 152136Hom.: 12 Cov.: 32
GnomAD3 exomes AF: 0.00157 AC: 369AN: 234962Hom.: 6 AF XY: 0.00123 AC XY: 157AN XY: 127718
GnomAD4 exome AF: 0.000617 AC: 882AN: 1430568Hom.: 15 Cov.: 29 AF XY: 0.000509 AC XY: 361AN XY: 708802
GnomAD4 genome AF: 0.00662 AC: 1008AN: 152254Hom.: 12 Cov.: 32 AF XY: 0.00627 AC XY: 467AN XY: 74452
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jun 05, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at