1-25686497-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_020379.4(MAN1C1):c.598C>T(p.Arg200Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000712 in 1,614,090 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_020379.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000191 AC: 29AN: 152206Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000596 AC: 15AN: 251486Hom.: 0 AF XY: 0.0000809 AC XY: 11AN XY: 135916
GnomAD4 exome AF: 0.0000588 AC: 86AN: 1461884Hom.: 0 Cov.: 30 AF XY: 0.0000633 AC XY: 46AN XY: 727242
GnomAD4 genome AF: 0.000191 AC: 29AN: 152206Hom.: 0 Cov.: 32 AF XY: 0.000242 AC XY: 18AN XY: 74364
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.598C>T (p.R200C) alteration is located in exon 2 (coding exon 2) of the MAN1C1 gene. This alteration results from a C to T substitution at nucleotide position 598, causing the arginine (R) at amino acid position 200 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