19-35295658-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4BS1_Supporting
The NM_002361.4(MAG):c.92C>T(p.Ser31Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000124 in 1,611,208 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 Uncertain significance (★).
Frequency
Consequence
NM_002361.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MAG | NM_002361.4 | c.92C>T | p.Ser31Leu | missense_variant | Exon 4 of 11 | ENST00000392213.8 | NP_002352.1 | |
MAG | NM_001199216.2 | c.17C>T | p.Ser6Leu | missense_variant | Exon 4 of 11 | NP_001186145.1 | ||
MAG | NM_080600.3 | c.92C>T | p.Ser31Leu | missense_variant | Exon 4 of 12 | NP_542167.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152162Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000281 AC: 7AN: 248940Hom.: 0 AF XY: 0.0000446 AC XY: 6AN XY: 134668
GnomAD4 exome AF: 0.0000123 AC: 18AN: 1459046Hom.: 0 Cov.: 31 AF XY: 0.0000138 AC XY: 10AN XY: 725918
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152162Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74338
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.92C>T (p.S31L) alteration is located in exon 4 (coding exon 2) of the MAG gene. This alteration results from a C to T substitution at nucleotide position 92, causing the serine (S) at amino acid position 31 to be replaced by a leucine (L). 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