16-722313-C-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_023933.3(ANTKMT):āc.464C>Gā(p.Pro155Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000162 in 1,608,300 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_023933.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ANTKMT | NM_023933.3 | c.464C>G | p.Pro155Arg | missense_variant | 5/5 | ENST00000569529.6 | |
ANTKMT | NM_001271285.2 | c.413C>G | p.Pro138Arg | missense_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ANTKMT | ENST00000569529.6 | c.464C>G | p.Pro155Arg | missense_variant | 5/5 | 1 | NM_023933.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152236Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000552 AC: 13AN: 235320Hom.: 0 AF XY: 0.0000543 AC XY: 7AN XY: 128918
GnomAD4 exome AF: 0.0000172 AC: 25AN: 1455946Hom.: 0 Cov.: 45 AF XY: 0.0000180 AC XY: 13AN XY: 723946
GnomAD4 genome AF: 0.00000656 AC: 1AN: 152354Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74510
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 19, 2024 | The c.464C>G (p.P155R) alteration is located in exon 5 (coding exon 5) of the FAM173A gene. This alteration results from a C to G substitution at nucleotide position 464, causing the proline (P) at amino acid position 155 to be replaced by an arginine (R). 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