1-25753562-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_020379.4(MAN1C1):c.913G>A(p.Val305Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000229 in 1,613,506 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/23 in silico tools predict 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 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MAN1C1 | NM_020379.4 | c.913G>A | p.Val305Met | missense_variant | 5/12 | ENST00000374332.9 | NP_065112.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MAN1C1 | ENST00000374332.9 | c.913G>A | p.Val305Met | missense_variant | 5/12 | 1 | NM_020379.4 | ENSP00000363452 | P1 | |
MAN1C1 | ENST00000263979.7 | c.373G>A | p.Val125Met | missense_variant | 6/13 | 5 | ENSP00000263979 | |||
MAN1C1 | ENST00000374329.1 | c.226G>A | p.Val76Met | missense_variant | 4/11 | 2 | ENSP00000363449 | |||
MAN1C1 | ENST00000473891.1 | n.311G>A | non_coding_transcript_exon_variant | 4/5 | 4 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152234Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000160 AC: 4AN: 250568Hom.: 0 AF XY: 0.00000738 AC XY: 1AN XY: 135496
GnomAD4 exome AF: 0.0000226 AC: 33AN: 1461272Hom.: 0 Cov.: 30 AF XY: 0.0000193 AC XY: 14AN XY: 726924
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152234Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74368
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 04, 2022 | The c.913G>A (p.V305M) alteration is located in exon 5 (coding exon 5) of the MAN1C1 gene. This alteration results from a G to A substitution at nucleotide position 913, causing the valine (V) at amino acid position 305 to be replaced by a methionine (M). 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