chr9-85588377-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001330701.2(AGTPBP1):c.2824C>T(p.Pro942Ser) variant causes a missense change. The variant allele was found at a frequency of 0.0000694 in 1,613,308 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000079 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000068 ( 0 hom. )
Consequence
AGTPBP1
NM_001330701.2 missense
NM_001330701.2 missense
Scores
1
8
8
Clinical Significance
Conservation
PhyloP100: 5.60
Genes affected
AGTPBP1 (HGNC:17258): (ATP/GTP binding carboxypeptidase 1) NNA1 is a zinc carboxypeptidase that contains nuclear localization signals and an ATP/GTP-binding motif that was initially cloned from regenerating spinal cord neurons of the mouse.[supplied by OMIM, Jul 2002]
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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=0.2737586).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AGTPBP1 | NM_001330701.2 | c.2824C>T | p.Pro942Ser | missense_variant | 21/26 | ENST00000357081.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AGTPBP1 | ENST00000357081.8 | c.2824C>T | p.Pro942Ser | missense_variant | 21/26 | 5 | NM_001330701.2 | P1 | |
AGTPBP1 | ENST00000376083.7 | c.2704C>T | p.Pro902Ser | missense_variant | 21/26 | 1 | |||
AGTPBP1 | ENST00000337006.8 | c.2980C>T | p.Pro994Ser | missense_variant | 20/25 | 5 | |||
AGTPBP1 | ENST00000628899.1 | c.2860C>T | p.Pro954Ser | missense_variant | 20/25 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000789 AC: 12AN: 152080Hom.: 0 Cov.: 32
GnomAD3 genomes
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GnomAD3 exomes AF: 0.000116 AC: 29AN: 250972Hom.: 0 AF XY: 0.000111 AC XY: 15AN XY: 135654
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GnomAD4 exome AF: 0.0000684 AC: 100AN: 1461110Hom.: 0 Cov.: 30 AF XY: 0.0000715 AC XY: 52AN XY: 726864
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GnomAD4 genome ? AF: 0.0000788 AC: 12AN: 152198Hom.: 0 Cov.: 32 AF XY: 0.0000672 AC XY: 5AN XY: 74400
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 11, 2022 | The c.2704C>T (p.P902S) alteration is located in exon 21 (coding exon 20) of the AGTPBP1 gene. This alteration results from a C to T substitution at nucleotide position 2704, causing the proline (P) at amino acid position 902 to be replaced by a serine (S). 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
Benign
Cadd
Uncertain
Dann
Uncertain
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;D;D;D
M_CAP
Benign
T
MetaRNN
Benign
T;T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
D;D;D;D;D
PrimateAI
Uncertain
T
PROVEAN
Pathogenic
D;.;D;.
REVEL
Benign
Sift
Uncertain
D;.;D;.
Sift4G
Uncertain
D;D;D;D
Polyphen
P;.;P;B
Vest4
MVP
MPC
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