X-152736238-T-C
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001166387.4(MAGEA12):āc.77T>Cā(p.Val26Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000174 in 1,209,697 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 15 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 7/11 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
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.77T>C | p.Val26Ala | missense_variant | 3/3 | ENST00000393869.8 | |
CSAG4 | NR_073432.1 | n.33+2379T>C | intron_variant, non_coding_transcript_variant | ||||
MAGEA12 | NM_001166386.3 | c.77T>C | p.Val26Ala | missense_variant | 3/3 | ||
MAGEA12 | NM_005367.7 | c.77T>C | p.Val26Ala | missense_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAGEA12 | ENST00000393869.8 | c.77T>C | p.Val26Ala | missense_variant | 3/3 | 2 | NM_001166387.4 | P1 | |
MAGEA12 | ENST00000357916.8 | c.77T>C | p.Val26Ala | missense_variant | 2/2 | 1 | P1 | ||
MAGEA12 | ENST00000393900.4 | c.77T>C | p.Val26Ala | missense_variant | 3/3 | 1 | P1 | ||
CSAG4 | ENST00000361201.8 | n.33+2379T>C | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.00000897 AC: 1AN: 111466Hom.: 0 Cov.: 23 AF XY: 0.0000297 AC XY: 1AN XY: 33640
GnomAD3 exomes AF: 0.0000601 AC: 11AN: 183087Hom.: 0 AF XY: 0.000103 AC XY: 7AN XY: 67719
GnomAD4 exome AF: 0.0000182 AC: 20AN: 1098179Hom.: 0 Cov.: 31 AF XY: 0.0000385 AC XY: 14AN XY: 363543
GnomAD4 genome AF: 0.00000897 AC: 1AN: 111518Hom.: 0 Cov.: 23 AF XY: 0.0000297 AC XY: 1AN XY: 33702
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 14, 2023 | The c.77T>C (p.V26A) alteration is located in exon 3 (coding exon 1) of the MAGEA12 gene. This alteration results from a T to C substitution at nucleotide position 77, causing the valine (V) at amino acid position 26 to be replaced by an alanine (A). 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