rs778001194
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001011548.1(MAGEA4):c.499G>A(p.Val167Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000149 in 1,210,525 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 6 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V167L) has been classified as Uncertain significance.
Frequency
Consequence
NM_001011548.1 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MAGEA4 | NM_001011548.1 | c.499G>A | p.Val167Met | missense_variant | Exon 3 of 3 | ENST00000276344.6 | NP_001011548.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000712 AC: 8AN: 112367Hom.: 0 Cov.: 24 AF XY: 0.000116 AC XY: 4AN XY: 34525
GnomAD3 exomes AF: 0.0000327 AC: 6AN: 183397Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 67853
GnomAD4 exome AF: 0.00000911 AC: 10AN: 1098106Hom.: 0 Cov.: 36 AF XY: 0.00000550 AC XY: 2AN XY: 363474
GnomAD4 genome AF: 0.0000712 AC: 8AN: 112419Hom.: 0 Cov.: 24 AF XY: 0.000116 AC XY: 4AN XY: 34587
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at