rs147529965
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 2P and 9B. PM2BP4_StrongBP6BS1
The NM_016219.5(MAN1B1):āc.337T>Cā(p.Phe113Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000247 in 1,613,970 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_016219.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MAN1B1 | NM_016219.5 | c.337T>C | p.Phe113Leu | missense_variant | 3/13 | ENST00000371589.9 | NP_057303.2 | |
MAN1B1 | XM_006716945.5 | c.337T>C | p.Phe113Leu | missense_variant | 3/12 | XP_006717008.1 | ||
MAN1B1 | NR_045720.2 | n.352T>C | non_coding_transcript_exon_variant | 3/13 | ||||
MAN1B1 | NR_045721.2 | n.483T>C | non_coding_transcript_exon_variant | 4/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MAN1B1 | ENST00000371589.9 | c.337T>C | p.Phe113Leu | missense_variant | 3/13 | 1 | NM_016219.5 | ENSP00000360645.4 |
Frequencies
GnomAD3 genomes AF: 0.00124 AC: 188AN: 152222Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000350 AC: 88AN: 251266Hom.: 1 AF XY: 0.000191 AC XY: 26AN XY: 135884
GnomAD4 exome AF: 0.000144 AC: 211AN: 1461630Hom.: 1 Cov.: 31 AF XY: 0.000103 AC XY: 75AN XY: 727098
GnomAD4 genome AF: 0.00123 AC: 188AN: 152340Hom.: 0 Cov.: 33 AF XY: 0.00125 AC XY: 93AN XY: 74492
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Jul 19, 2017 | - - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Jul 20, 2017 | - - |
Rafiq syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Oct 18, 2022 | - - |
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 09, 2021 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
MAN1B1-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Apr 15, 2022 | 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
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at