chr6-37646228-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_153487.4(MDGA1):c.2194A>G(p.Met732Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000119 in 1,591,230 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_153487.4 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 |
---|---|---|---|---|---|---|---|
MDGA1 | NM_153487.4 | c.2194A>G | p.Met732Val | missense_variant | 11/17 | ENST00000434837.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MDGA1 | ENST00000434837.8 | c.2194A>G | p.Met732Val | missense_variant | 11/17 | 1 | NM_153487.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152170Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000516 AC: 12AN: 232750Hom.: 0 AF XY: 0.0000557 AC XY: 7AN XY: 125776
GnomAD4 exome AF: 0.0000118 AC: 17AN: 1439060Hom.: 0 Cov.: 31 AF XY: 0.0000112 AC XY: 8AN XY: 712546
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152170Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74332
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 28, 2023 | The c.2194A>G (p.M732V) alteration is located in exon 11 (coding exon 11) of the MDGA1 gene. This alteration results from a A to G substitution at nucleotide position 2194, causing the methionine (M) at amino acid position 732 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