rs113328438
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_002361.4(MAG):āc.409A>Gā(p.Ile137Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00196 in 1,573,478 control chromosomes in the GnomAD database, including 58 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Consequence
NM_002361.4 missense
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 | UniProt |
---|---|---|---|---|---|---|---|
MAG | NM_002361.4 | c.409A>G | p.Ile137Val | missense_variant | 4/11 | ENST00000392213.8 | |
MAG | NM_001199216.2 | c.334A>G | p.Ile112Val | missense_variant | 4/11 | ||
MAG | NM_080600.3 | c.409A>G | p.Ile137Val | missense_variant | 4/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAG | ENST00000392213.8 | c.409A>G | p.Ile137Val | missense_variant | 4/11 | 1 | NM_002361.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00995 AC: 1515AN: 152194Hom.: 37 Cov.: 32
GnomAD3 exomes AF: 0.00286 AC: 625AN: 218356Hom.: 10 AF XY: 0.00202 AC XY: 238AN XY: 117936
GnomAD4 exome AF: 0.00109 AC: 1556AN: 1421166Hom.: 20 Cov.: 32 AF XY: 0.000972 AC XY: 682AN XY: 701790
GnomAD4 genome ? AF: 0.0100 AC: 1528AN: 152312Hom.: 38 Cov.: 32 AF XY: 0.00925 AC XY: 689AN XY: 74486
ClinVar
Submissions by phenotype
Hereditary spastic paraplegia 75 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 09, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at