19-43015293-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_002785.3(PSG11):c.787G>T(p.Ala263Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000193 in 1,610,316 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002785.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PSG11 | NM_002785.3 | c.787G>T | p.Ala263Ser | missense_variant | 4/6 | ENST00000320078.12 | NP_002776.3 | |
PSG11 | NM_001113410.2 | c.421G>T | p.Ala141Ser | missense_variant | 3/5 | NP_001106881.1 | ||
PSG11 | NM_203287.2 | c.421G>T | p.Ala141Ser | missense_variant | 3/5 | NP_976032.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000198 AC: 3AN: 151368Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000279 AC: 7AN: 251204Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135750
GnomAD4 exome AF: 0.0000192 AC: 28AN: 1458948Hom.: 1 Cov.: 34 AF XY: 0.0000207 AC XY: 15AN XY: 725878
GnomAD4 genome AF: 0.0000198 AC: 3AN: 151368Hom.: 0 Cov.: 32 AF XY: 0.0000271 AC XY: 2AN XY: 73908
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 17, 2023 | The c.787G>T (p.A263S) alteration is located in exon 4 (coding exon 4) of the PSG11 gene. This alteration results from a G to T substitution at nucleotide position 787, causing the alanine (A) at amino acid position 263 to be replaced by a serine (S). 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