15-94298381-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_001385001.1(MCTP2):c.116G>A(p.Arg39Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00135 in 1,614,084 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. R39R) has been classified as Benign.
Frequency
Consequence
NM_001385001.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MCTP2 | NM_001385001.1 | c.116G>A | p.Arg39Gln | missense_variant | 2/23 | ENST00000357742.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MCTP2 | ENST00000357742.10 | c.116G>A | p.Arg39Gln | missense_variant | 2/23 | 1 | NM_001385001.1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000861 AC: 131AN: 152090Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00122 AC: 307AN: 251314Hom.: 1 AF XY: 0.00124 AC XY: 169AN XY: 135804
GnomAD4 exome AF: 0.00140 AC: 2046AN: 1461876Hom.: 3 Cov.: 32 AF XY: 0.00130 AC XY: 943AN XY: 727242
GnomAD4 genome ? AF: 0.000861 AC: 131AN: 152208Hom.: 0 Cov.: 31 AF XY: 0.000833 AC XY: 62AN XY: 74420
ClinVar
Submissions by phenotype
MCTP2-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Aug 02, 2023 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at