5-109774901-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_002372.4(MAN2A1):c.1310T>C(p.Leu437Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000416 in 1,611,144 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 Uncertain significance (★).
Frequency
Consequence
NM_002372.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MAN2A1 | NM_002372.4 | c.1310T>C | p.Leu437Ser | missense_variant | 8/22 | ENST00000261483.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAN2A1 | ENST00000261483.5 | c.1310T>C | p.Leu437Ser | missense_variant | 8/22 | 1 | NM_002372.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000132 AC: 2AN: 152074Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000798 AC: 20AN: 250496Hom.: 0 AF XY: 0.0000960 AC XY: 13AN XY: 135424
GnomAD4 exome AF: 0.0000445 AC: 65AN: 1459070Hom.: 1 Cov.: 30 AF XY: 0.0000661 AC XY: 48AN XY: 725970
GnomAD4 genome ? AF: 0.0000132 AC: 2AN: 152074Hom.: 0 Cov.: 31 AF XY: 0.0000269 AC XY: 2AN XY: 74282
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 31, 2022 | The c.1310T>C (p.L437S) alteration is located in exon 8 (coding exon 8) of the MAN2A1 gene. This alteration results from a T to C substitution at nucleotide position 1310, causing the leucine (L) at amino acid position 437 to be replaced by a serine (S). 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