X-152736678-G-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001166387.4(MAGEA12):c.517G>A(p.Gly173Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000669 in 1,210,128 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 37 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 8/12 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001166387.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MAGEA12 | NM_001166387.4 | c.517G>A | p.Gly173Ser | missense_variant | 3/3 | ENST00000393869.8 | |
CSAG4 | NR_073432.1 | n.33+2819G>A | intron_variant, non_coding_transcript_variant | ||||
MAGEA12 | NM_001166386.3 | c.517G>A | p.Gly173Ser | missense_variant | 3/3 | ||
MAGEA12 | NM_005367.7 | c.517G>A | p.Gly173Ser | missense_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAGEA12 | ENST00000393869.8 | c.517G>A | p.Gly173Ser | missense_variant | 3/3 | 2 | NM_001166387.4 | P1 | |
MAGEA12 | ENST00000357916.8 | c.517G>A | p.Gly173Ser | missense_variant | 2/2 | 1 | P1 | ||
MAGEA12 | ENST00000393900.4 | c.517G>A | p.Gly173Ser | missense_variant | 3/3 | 1 | P1 | ||
CSAG4 | ENST00000361201.8 | n.33+2819G>A | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000179 AC: 2AN: 111885Hom.: 0 Cov.: 23 AF XY: 0.0000293 AC XY: 1AN XY: 34081
GnomAD3 exomes AF: 0.0000602 AC: 11AN: 182864Hom.: 0 AF XY: 0.0000742 AC XY: 5AN XY: 67422
GnomAD4 exome AF: 0.0000719 AC: 79AN: 1098243Hom.: 0 Cov.: 32 AF XY: 0.0000990 AC XY: 36AN XY: 363613
GnomAD4 genome ? AF: 0.0000179 AC: 2AN: 111885Hom.: 0 Cov.: 23 AF XY: 0.0000293 AC XY: 1AN XY: 34081
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 14, 2021 | The c.517G>A (p.G173S) alteration is located in exon 3 (coding exon 1) of the MAGEA12 gene. This alteration results from a G to A substitution at nucleotide position 517, causing the glycine (G) at amino acid position 173 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