chr5-109767648-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_002372.4(MAN2A1):c.949G>A(p.Ala317Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0007 in 1,613,690 control chromosomes in the GnomAD database, including 3 homozygotes. 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 (★).
Frequency
Consequence
NM_002372.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MAN2A1 | NM_002372.4 | c.949G>A | p.Ala317Thr | missense_variant | 6/22 | ENST00000261483.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAN2A1 | ENST00000261483.5 | c.949G>A | p.Ala317Thr | missense_variant | 6/22 | 1 | NM_002372.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000513 AC: 78AN: 152120Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000355 AC: 89AN: 251012Hom.: 0 AF XY: 0.000317 AC XY: 43AN XY: 135640
GnomAD4 exome AF: 0.000720 AC: 1052AN: 1461452Hom.: 3 Cov.: 31 AF XY: 0.000682 AC XY: 496AN XY: 727048
GnomAD4 genome ? AF: 0.000512 AC: 78AN: 152238Hom.: 0 Cov.: 32 AF XY: 0.000497 AC XY: 37AN XY: 74420
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 15, 2021 | The c.949G>A (p.A317T) alteration is located in exon 6 (coding exon 6) of the MAN2A1 gene. This alteration results from a G to A substitution at nucleotide position 949, causing the alanine (A) at amino acid position 317 to be replaced by a threonine (T). 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