chr19-12661333-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_000528.4(MAN2B1):c.953C>T(p.Ser318Leu) variant causes a missense change. The variant allele was found at a frequency of 0.0000031 in 1,613,900 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (no stars). Synonymous variant affecting the same amino acid position (i.e. S318S) has been classified as Likely benign.
Frequency
Consequence
NM_000528.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MAN2B1 | NM_000528.4 | c.953C>T | p.Ser318Leu | missense_variant | 7/24 | ENST00000456935.7 | |
MAN2B1 | NM_001173498.2 | c.953C>T | p.Ser318Leu | missense_variant | 7/24 | ||
MAN2B1 | XM_005259913.3 | c.953C>T | p.Ser318Leu | missense_variant | 7/24 | ||
MAN2B1 | XM_047438841.1 | c.-66C>T | 5_prime_UTR_variant | 1/17 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAN2B1 | ENST00000456935.7 | c.953C>T | p.Ser318Leu | missense_variant | 7/24 | 1 | NM_000528.4 | A1 | |
MAN2B1 | ENST00000221363.8 | c.953C>T | p.Ser318Leu | missense_variant | 7/24 | 1 | P4 | ||
MAN2B1 | ENST00000462144.1 | n.146C>T | non_coding_transcript_exon_variant | 2/2 | 3 | ||||
MAN2B1 | ENST00000466794.5 | n.935C>T | non_coding_transcript_exon_variant | 7/22 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152198Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251486Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135922
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461702Hom.: 0 Cov.: 33 AF XY: 0.00000275 AC XY: 2AN XY: 727144
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152198Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74350
ClinVar
Submissions by phenotype
Deficiency of alpha-mannosidase Uncertain:1
Uncertain significance, no assertion criteria provided | literature only | ClinVar Staff, National Center for Biotechnology Information (NCBI) | Jun 07, 2012 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at