1-25771760-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_020379.4(MAN1C1):c.1245C>T(p.Tyr415=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000465 in 1,612,964 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 Likely benign (★).
Frequency
Genomes: 𝑓 0.000046 ( 0 hom., cov: 34)
Exomes 𝑓: 0.000047 ( 0 hom. )
Consequence
MAN1C1
NM_020379.4 synonymous
NM_020379.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.30
Genes affected
MAN1C1 (HGNC:19080): (mannosidase alpha class 1C member 1) Predicted to enable mannosyl-oligosaccharide 1,2-alpha-mannosidase activity. Predicted to be involved in N-glycan processing. Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.48).
BP6
?
Variant 1-25771760-C-T is Benign according to our data. Variant chr1-25771760-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 3051149.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-1.3 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MAN1C1 | NM_020379.4 | c.1245C>T | p.Tyr415= | synonymous_variant | 8/12 | ENST00000374332.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAN1C1 | ENST00000374332.9 | c.1245C>T | p.Tyr415= | synonymous_variant | 8/12 | 1 | NM_020379.4 | P1 | |
MAN1C1 | ENST00000263979.7 | c.705C>T | p.Tyr235= | synonymous_variant | 9/13 | 5 | |||
MAN1C1 | ENST00000374329.1 | c.558C>T | p.Tyr186= | synonymous_variant | 7/11 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000460 AC: 7AN: 152228Hom.: 0 Cov.: 34
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GnomAD3 exomes AF: 0.0000756 AC: 19AN: 251284Hom.: 0 AF XY: 0.0000883 AC XY: 12AN XY: 135838
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GnomAD4 exome AF: 0.0000466 AC: 68AN: 1460618Hom.: 0 Cov.: 31 AF XY: 0.0000537 AC XY: 39AN XY: 726700
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GnomAD4 genome ? AF: 0.0000459 AC: 7AN: 152346Hom.: 0 Cov.: 34 AF XY: 0.0000671 AC XY: 5AN XY: 74484
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
MAN1C1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jan 09, 2020 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
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Dann
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at