rs17855116
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_018109.4(MTPAP):c.1637G>A(p.Ser546Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00166 in 1,614,140 control chromosomes in the GnomAD database, including 12 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_018109.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MTPAP | NM_018109.4 | c.1637G>A | p.Ser546Asn | missense_variant | 9/9 | ENST00000263063.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MTPAP | ENST00000263063.9 | c.1637G>A | p.Ser546Asn | missense_variant | 9/9 | 1 | NM_018109.4 | P1 | |
MTPAP | ENST00000488290.5 | n.3392G>A | non_coding_transcript_exon_variant | 17/17 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00206 AC: 313AN: 152148Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.00247 AC: 620AN: 251390Hom.: 7 AF XY: 0.00236 AC XY: 321AN XY: 135868
GnomAD4 exome AF: 0.00162 AC: 2368AN: 1461874Hom.: 10 Cov.: 31 AF XY: 0.00162 AC XY: 1176AN XY: 727244
GnomAD4 genome ? AF: 0.00206 AC: 313AN: 152266Hom.: 2 Cov.: 32 AF XY: 0.00250 AC XY: 186AN XY: 74442
ClinVar
Submissions by phenotype
not specified Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Mar 03, 2017 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Sep 16, 2015 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 22, 2024 | - - |
MTPAP-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jun 19, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at