X-49164743-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_024859.4(MAGIX):c.233C>T(p.Thr78Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000826 in 1,210,504 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 4 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_024859.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MAGIX | NM_024859.4 | c.233C>T | p.Thr78Ile | missense_variant | Exon 3 of 6 | ENST00000595224.6 | NP_079135.3 | |
MAGIX | NM_001099681.2 | c.233C>T | p.Thr78Ile | missense_variant | Exon 3 of 5 | NP_001093151.2 | ||
MAGIX | NM_001099682.2 | c.233C>T | p.Thr78Ile | missense_variant | Exon 3 of 5 | NP_001093152.2 | ||
MAGIX | NM_001395401.1 | c.-18C>T | 5_prime_UTR_variant | Exon 3 of 5 | NP_001382330.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000178 AC: 2AN: 112595Hom.: 0 Cov.: 24 AF XY: 0.0000288 AC XY: 1AN XY: 34761
GnomAD3 exomes AF: 0.0000608 AC: 11AN: 180931Hom.: 0 AF XY: 0.0000595 AC XY: 4AN XY: 67221
GnomAD4 exome AF: 0.00000729 AC: 8AN: 1097909Hom.: 0 Cov.: 30 AF XY: 0.00000826 AC XY: 3AN XY: 363339
GnomAD4 genome AF: 0.0000178 AC: 2AN: 112595Hom.: 0 Cov.: 24 AF XY: 0.0000288 AC XY: 1AN XY: 34761
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.233C>T (p.T78I) alteration is located in exon 3 (coding exon 3) of the MAGIX gene. This alteration results from a C to T substitution at nucleotide position 233, causing the threonine (T) at amino acid position 78 to be replaced by an isoleucine (I). 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