chr5-109713532-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_002372.4(MAN2A1):c.148A>G(p.Met50Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000061 in 1,607,528 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Uncertain significance (★).
Frequency
Consequence
NM_002372.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MAN2A1 | NM_002372.4 | c.148A>G | p.Met50Val | missense_variant | 2/22 | ENST00000261483.5 | |
MAN2A1 | XM_017009472.2 | c.1A>G | p.Met1? | start_lost | 2/22 | ||
MAN2A1 | XM_011543395.4 | c.148A>G | p.Met50Val | missense_variant | 2/17 | ||
MAN2A1 | XR_007058604.1 | n.639A>G | non_coding_transcript_exon_variant | 2/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAN2A1 | ENST00000261483.5 | c.148A>G | p.Met50Val | missense_variant | 2/22 | 1 | NM_002372.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000118 AC: 18AN: 152202Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000362 AC: 9AN: 248478Hom.: 0 AF XY: 0.0000446 AC XY: 6AN XY: 134548
GnomAD4 exome AF: 0.0000550 AC: 80AN: 1455208Hom.: 0 Cov.: 33 AF XY: 0.0000581 AC XY: 42AN XY: 722628
GnomAD4 genome ? AF: 0.000118 AC: 18AN: 152320Hom.: 0 Cov.: 32 AF XY: 0.0000805 AC XY: 6AN XY: 74496
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 11, 2023 | The c.148A>G (p.M50V) alteration is located in exon 2 (coding exon 2) of the MAN2A1 gene. This alteration results from a A to G substitution at nucleotide position 148, causing the methionine (M) at amino acid position 50 to be replaced by a valine (V). 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