chr4-98128451-G-T
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Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_174952.3(STPG2):c.364C>A(p.Pro122Thr) variant causes a missense change. The variant allele was found at a frequency of 0.0000416 in 1,610,132 control chromosomes in the GnomAD database, including 3 homozygotes. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000046 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000041 ( 3 hom. )
Consequence
STPG2
NM_174952.3 missense
NM_174952.3 missense
Scores
7
5
7
Clinical Significance
Conservation
PhyloP100: 5.30
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
BS2
High Homozygotes in GnomAdExome4 at 3 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
STPG2 | NM_174952.3 | c.364C>A | p.Pro122Thr | missense_variant | 3/11 | ENST00000295268.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
STPG2 | ENST00000295268.4 | c.364C>A | p.Pro122Thr | missense_variant | 3/11 | 1 | NM_174952.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152094Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000888 AC: 22AN: 247836Hom.: 0 AF XY: 0.000119 AC XY: 16AN XY: 133902
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GnomAD4 exome AF: 0.0000412 AC: 60AN: 1457920Hom.: 3 Cov.: 32 AF XY: 0.0000607 AC XY: 44AN XY: 725172
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GnomAD4 genome AF: 0.0000460 AC: 7AN: 152212Hom.: 0 Cov.: 32 AF XY: 0.0000672 AC XY: 5AN XY: 74412
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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 | Jul 14, 2023 | The c.364C>A (p.P122T) alteration is located in exon 3 (coding exon 3) of the STPG2 gene. This alteration results from a C to A substitution at nucleotide position 364, causing the proline (P) at amino acid position 122 to be replaced by a threonine (T). 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
Uncertain
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
T
Eigen
Pathogenic
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Benign
T
M_CAP
Benign
T
MetaRNN
Uncertain
T
MetaSVM
Benign
T
MutationAssessor
Pathogenic
M
MutationTaster
Benign
D
PrimateAI
Benign
T
PROVEAN
Pathogenic
D
REVEL
Uncertain
Sift
Pathogenic
D
Sift4G
Pathogenic
D
Polyphen
D
Vest4
MVP
MPC
ClinPred
D
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