16-721919-A-G
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Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_023933.3(ANTKMT):āc.386A>Gā(p.Tyr129Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000114 in 1,572,664 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Genomes: š 0.00013 ( 0 hom., cov: 35)
Exomes š: 0.00011 ( 0 hom. )
Consequence
ANTKMT
NM_023933.3 missense
NM_023933.3 missense
Scores
4
7
8
Clinical Significance
Conservation
PhyloP100: 1.24
Genes affected
ANTKMT (HGNC:14152): (adenine nucleotide translocase lysine methyltransferase) Enables protein-lysine N-methyltransferase activity. Involved in peptidyl-lysine trimethylation. Located in mitochondrion. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ANTKMT | NM_023933.3 | c.386A>G | p.Tyr129Cys | missense_variant | 3/5 | ENST00000569529.6 | |
ANTKMT | NM_001271285.2 | c.386A>G | p.Tyr129Cys | missense_variant | 3/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ANTKMT | ENST00000569529.6 | c.386A>G | p.Tyr129Cys | missense_variant | 3/5 | 1 | NM_023933.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000131 AC: 20AN: 152176Hom.: 0 Cov.: 35
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GnomAD3 exomes AF: 0.000105 AC: 19AN: 181632Hom.: 0 AF XY: 0.0000995 AC XY: 10AN XY: 100496
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GnomAD4 exome AF: 0.000113 AC: 160AN: 1420370Hom.: 0 Cov.: 61 AF XY: 0.000116 AC XY: 82AN XY: 704360
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GnomAD4 genome AF: 0.000131 AC: 20AN: 152294Hom.: 0 Cov.: 35 AF XY: 0.000107 AC XY: 8AN XY: 74472
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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 18, 2022 | The c.386A>G (p.Y129C) alteration is located in exon 3 (coding exon 3) of the FAM173A gene. This alteration results from a A to G substitution at nucleotide position 386, causing the tyrosine (Y) at amino acid position 129 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
DEOGEN2
Benign
T;T;T
Eigen
Uncertain
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;D;D
M_CAP
Benign
D
MetaRNN
Uncertain
D;D;D
MetaSVM
Benign
T
MutationAssessor
Uncertain
M;.;.
MutationTaster
Benign
D;D;D;D;D
PrimateAI
Uncertain
T
PROVEAN
Pathogenic
D;D;D
REVEL
Benign
Sift
Pathogenic
D;D;D
Sift4G
Pathogenic
D;D;D
Polyphen
D;.;.
Vest4
MutPred
Loss of catalytic residue at Y129 (P = 0.092);Loss of catalytic residue at Y129 (P = 0.092);Loss of catalytic residue at Y129 (P = 0.092);
MVP
MPC
ClinPred
D
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
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