chr11-77842549-G-C
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Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_024684.4(AAMDC):āc.53G>Cā(p.Gly18Ala) variant causes a missense change. The variant allele was found at a frequency of 0.000512 in 1,614,000 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Genomes: š 0.00031 ( 0 hom., cov: 32)
Exomes š: 0.00053 ( 1 hom. )
Consequence
AAMDC
NM_024684.4 missense
NM_024684.4 missense
Scores
2
12
5
Clinical Significance
Conservation
PhyloP100: 6.61
Genes affected
AAMDC (HGNC:30205): (adipogenesis associated Mth938 domain containing) Predicted to be involved in positive regulation of fat cell differentiation. Predicted to act upstream of or within negative regulation of apoptotic process and positive regulation of transcription by RNA polymerase II. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 1 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.2949015).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AAMDC | NM_024684.4 | c.53G>C | p.Gly18Ala | missense_variant | 2/4 | ENST00000393427.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AAMDC | ENST00000393427.7 | c.53G>C | p.Gly18Ala | missense_variant | 2/4 | 1 | NM_024684.4 | P1 | |
ENST00000525594.1 | n.112-12422C>G | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes AF: 0.000309 AC: 47AN: 152120Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000338 AC: 85AN: 251134Hom.: 0 AF XY: 0.000346 AC XY: 47AN XY: 135734
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GnomAD4 exome AF: 0.000533 AC: 779AN: 1461762Hom.: 1 Cov.: 30 AF XY: 0.000531 AC XY: 386AN XY: 727170
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GnomAD4 genome AF: 0.000309 AC: 47AN: 152238Hom.: 0 Cov.: 32 AF XY: 0.000255 AC XY: 19AN XY: 74404
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 05, 2023 | The c.53G>C (p.G18A) alteration is located in exon 2 (coding exon 1) of the AAMDC gene. This alteration results from a G to C substitution at nucleotide position 53, causing the glycine (G) at amino acid position 18 to be replaced by an alanine (A). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Uncertain
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Uncertain
.;D;D;.;.;.;T;T;D
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;.;D;D;.;D;D;D;D
M_CAP
Benign
T
MetaRNN
Benign
T;T;T;T;T;T;T;T;T
MetaSVM
Uncertain
D
MutationAssessor
Uncertain
M;M;M;.;.;.;.;.;.
MutationTaster
Benign
D;D;D;D;D;D;D;D
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D;D;D;D;D;.;D;N;D
REVEL
Uncertain
Sift
Uncertain
D;D;D;D;D;.;D;D;D
Sift4G
Uncertain
D;T;T;D;D;D;D;D;T
Polyphen
D;P;P;D;.;.;.;.;.
Vest4
MVP
MPC
0.074
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at