2-113182488-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_012455.3(PSD4):c.32C>A(p.Pro11His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000044 in 1,613,638 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 (★).
Frequency
Consequence
NM_012455.3 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 |
---|---|---|---|---|---|---|---|
PSD4 | NM_012455.3 | c.32C>A | p.Pro11His | missense_variant | 2/17 | ENST00000245796.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PSD4 | ENST00000245796.11 | c.32C>A | p.Pro11His | missense_variant | 2/17 | 1 | NM_012455.3 | P3 |
Frequencies
GnomAD3 genomes AF: 0.0000591 AC: 9AN: 152206Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000112 AC: 28AN: 250560Hom.: 0 AF XY: 0.0000665 AC XY: 9AN XY: 135376
GnomAD4 exome AF: 0.0000424 AC: 62AN: 1461432Hom.: 0 Cov.: 30 AF XY: 0.0000371 AC XY: 27AN XY: 727018
GnomAD4 genome AF: 0.0000591 AC: 9AN: 152206Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74360
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 30, 2023 | The c.32C>A (p.P11H) alteration is located in exon 2 (coding exon 1) of the PSD4 gene. This alteration results from a C to A substitution at nucleotide position 32, causing the proline (P) at amino acid position 11 to be replaced by a histidine (H). 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