X-54810072-A-G
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_177433.3(MAGED2):āc.396A>Gā(p.Thr132Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.373 in 1,203,510 control chromosomes in the GnomAD database, including 60,298 homozygotes. There are 145,279 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Consequence
NM_177433.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MAGED2 | NM_177433.3 | c.396A>G | p.Thr132Thr | synonymous_variant | Exon 3 of 13 | ENST00000375068.6 | NP_803182.1 | |
MAGED2 | NM_014599.6 | c.396A>G | p.Thr132Thr | synonymous_variant | Exon 3 of 13 | NP_055414.2 | ||
MAGED2 | NM_201222.3 | c.396A>G | p.Thr132Thr | synonymous_variant | Exon 3 of 13 | NP_957516.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.446 AC: 48518AN: 108902Hom.: 8808 Cov.: 21 AF XY: 0.435 AC XY: 13592AN XY: 31246
GnomAD3 exomes AF: 0.400 AC: 69792AN: 174666Hom.: 10295 AF XY: 0.383 AC XY: 23198AN XY: 60506
GnomAD4 exome AF: 0.366 AC: 400152AN: 1094553Hom.: 51496 Cov.: 33 AF XY: 0.365 AC XY: 131637AN XY: 360431
GnomAD4 genome AF: 0.446 AC: 48552AN: 108957Hom.: 8802 Cov.: 21 AF XY: 0.436 AC XY: 13642AN XY: 31311
ClinVar
Submissions by phenotype
not provided Benign:3
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Bartter disease type 5 Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at