2-134338268-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_002410.5(MGAT5):c.655C>T(p.Arg219Cys) variant causes a missense change. The variant allele was found at a frequency of 0.00000757 in 1,585,382 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002410.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152138Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000397 AC: 9AN: 226712Hom.: 0 AF XY: 0.0000163 AC XY: 2AN XY: 122820
GnomAD4 exome AF: 0.00000558 AC: 8AN: 1433244Hom.: 0 Cov.: 30 AF XY: 0.00000562 AC XY: 4AN XY: 711562
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152138Hom.: 0 Cov.: 33 AF XY: 0.0000538 AC XY: 4AN XY: 74312
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.655C>T (p.R219C) alteration is located in exon 1 (coding exon 1) of the MGAT5 gene. This alteration results from a C to T substitution at nucleotide position 655, causing the arginine (R) at amino acid position 219 to be replaced by a cysteine (C). 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