chr1-25753563-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_020379.4(MAN1C1):c.914T>C(p.Val305Ala) variant causes a missense change. The variant allele was found at a frequency of 0.000000684 in 1,461,232 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V305M) has been classified 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
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MAN1C1 | NM_020379.4 | c.914T>C | p.Val305Ala | missense_variant | 5/12 | ENST00000374332.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAN1C1 | ENST00000374332.9 | c.914T>C | p.Val305Ala | missense_variant | 5/12 | 1 | NM_020379.4 | P1 | |
MAN1C1 | ENST00000263979.7 | c.374T>C | p.Val125Ala | missense_variant | 6/13 | 5 | |||
MAN1C1 | ENST00000374329.1 | c.227T>C | p.Val76Ala | missense_variant | 4/11 | 2 | |||
MAN1C1 | ENST00000473891.1 | n.312T>C | non_coding_transcript_exon_variant | 4/5 | 4 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461232Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1AN XY: 726918
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 18, 2023 | The c.914T>C (p.V305A) alteration is located in exon 5 (coding exon 5) of the MAN1C1 gene. This alteration results from a T to C substitution at nucleotide position 914, causing the valine (V) at amino acid position 305 to be replaced by an alanine (A). 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
Publications
No publications associated with this variant yet.