chrX-152736747-G-C
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_001166387.4(MAGEA12):c.586G>C(p.Val196Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000909 in 1,210,228 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. 7/10 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
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MAGEA12 | NM_001166387.4 | c.586G>C | p.Val196Leu | missense_variant | 3/3 | ENST00000393869.8 | |
CSAG4 | NR_073432.1 | n.33+2888G>C | intron_variant, non_coding_transcript_variant | ||||
MAGEA12 | NM_001166386.3 | c.586G>C | p.Val196Leu | missense_variant | 3/3 | ||
MAGEA12 | NM_005367.7 | c.586G>C | p.Val196Leu | missense_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAGEA12 | ENST00000393869.8 | c.586G>C | p.Val196Leu | missense_variant | 3/3 | 2 | NM_001166387.4 | P1 | |
MAGEA12 | ENST00000357916.8 | c.586G>C | p.Val196Leu | missense_variant | 2/2 | 1 | P1 | ||
MAGEA12 | ENST00000393900.4 | c.586G>C | p.Val196Leu | missense_variant | 3/3 | 1 | P1 | ||
CSAG4 | ENST00000361201.8 | n.33+2888G>C | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000893 AC: 1AN: 111966Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34146
GnomAD3 exomes AF: 0.00000554 AC: 1AN: 180416Hom.: 0 AF XY: 0.0000152 AC XY: 1AN XY: 65996
GnomAD4 exome AF: 0.00000911 AC: 10AN: 1098262Hom.: 0 Cov.: 32 AF XY: 0.0000165 AC XY: 6AN XY: 363618
GnomAD4 genome ? AF: 0.00000893 AC: 1AN: 111966Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34146
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 26, 2022 | The c.586G>C (p.V196L) alteration is located in exon 3 (coding exon 1) of the MAGEA12 gene. This alteration results from a G to C substitution at nucleotide position 586, causing the valine (V) at amino acid position 196 to be replaced by a leucine (L). 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