1-117420608-A-G
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Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_006699.5(MAN1A2):āc.814A>Gā(p.Ile272Val) variant causes a missense change. The variant allele was found at a frequency of 0.0000105 in 1,612,960 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 (ā ).
Frequency
Genomes: š 0.000039 ( 0 hom., cov: 32)
Exomes š: 0.0000075 ( 0 hom. )
Consequence
MAN1A2
NM_006699.5 missense
NM_006699.5 missense
Scores
1
2
16
Clinical Significance
Conservation
PhyloP100: 5.43
Genes affected
MAN1A2 (HGNC:6822): (mannosidase alpha class 1A member 2) Alpha-mannosidases function at different stages of N-glycan maturation in mammalian cells. See MAN2A1 (MIM 154582) for general information.[supplied by OMIM, Mar 2008]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 1 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.2913651).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MAN1A2 | NM_006699.5 | c.814A>G | p.Ile272Val | missense_variant | 5/13 | ENST00000356554.7 | NP_006690.1 | |
MAN1A2 | XM_006710302.4 | c.814A>G | p.Ile272Val | missense_variant | 5/14 | XP_006710365.1 | ||
MAN1A2 | XM_011540536.4 | c.814A>G | p.Ile272Val | missense_variant | 5/13 | XP_011538838.1 | ||
MAN1A2 | XM_017000115.2 | c.814A>G | p.Ile272Val | missense_variant | 5/7 | XP_016855604.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MAN1A2 | ENST00000356554.7 | c.814A>G | p.Ile272Val | missense_variant | 5/13 | 1 | NM_006699.5 | ENSP00000348959.3 | ||
MAN1A2 | ENST00000449370.6 | c.10A>G | p.Ile4Val | missense_variant | 1/9 | 2 | ENSP00000412706.2 | |||
MAN1A2 | ENST00000482811.1 | n.702A>G | non_coding_transcript_exon_variant | 3/3 | 4 |
Frequencies
GnomAD3 genomes AF: 0.0000395 AC: 6AN: 152048Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000159 AC: 4AN: 250898Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135628
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GnomAD4 exome AF: 0.00000753 AC: 11AN: 1460912Hom.: 0 Cov.: 29 AF XY: 0.00000826 AC XY: 6AN XY: 726760
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GnomAD4 genome AF: 0.0000395 AC: 6AN: 152048Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74256
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 26, 2022 | The c.814A>G (p.I272V) alteration is located in exon 5 (coding exon 5) of the MAN1A2 gene. This alteration results from a A to G substitution at nucleotide position 814, causing the isoleucine (I) at amino acid position 272 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D
M_CAP
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Benign
N
PrimateAI
Uncertain
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Benign
T
Sift4G
Benign
T
Polyphen
B
Vest4
MutPred
Gain of methylation at R270 (P = 0.1);
MVP
MPC
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at