chr5-129764902-C-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP6
The NM_001257308.2(MINAR2):c.412C>T(p.Arg138Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000258 in 1,323,974 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 Likely benign (no stars).
Frequency
Consequence
NM_001257308.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MINAR2 | ENST00000564719.2 | c.412C>T | p.Arg138Trp | missense_variant | Exon 3 of 3 | 5 | NM_001257308.2 | ENSP00000454268.1 | ||
ENSG00000251680 | ENST00000503616.5 | n.122-2233G>A | intron_variant | Intron 2 of 4 | 3 | |||||
ENSG00000251680 | ENST00000515569.1 | n.286-2233G>A | intron_variant | Intron 3 of 3 | 2 | |||||
ENSG00000251680 | ENST00000653455.1 | n.94-2233G>A | intron_variant | Intron 1 of 3 |
Frequencies
GnomAD3 genomes AF: 0.00128 AC: 195AN: 152056Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000262 AC: 10AN: 38108Hom.: 0 AF XY: 0.000298 AC XY: 6AN XY: 20118
GnomAD4 exome AF: 0.000123 AC: 144AN: 1171800Hom.: 0 Cov.: 30 AF XY: 0.0000995 AC XY: 56AN XY: 562670
GnomAD4 genome AF: 0.00129 AC: 197AN: 152174Hom.: 0 Cov.: 32 AF XY: 0.00137 AC XY: 102AN XY: 74396
ClinVar
Submissions by phenotype
MINAR2-related condition Benign:1
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