chr11-61204153-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_001079807.4(PGA3):c.103C>T(p.Arg35Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. 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_001079807.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PGA3 | ENST00000325558.11 | c.103C>T | p.Arg35Cys | missense_variant | Exon 2 of 9 | 1 | NM_001079807.4 | ENSP00000322192.6 | ||
PGA3 | ENST00000535551.1 | n.847C>T | non_coding_transcript_exon_variant | Exon 1 of 3 | 3 | |||||
PGA3 | ENST00000537954.5 | n.153C>T | non_coding_transcript_exon_variant | Exon 2 of 2 | 2 | |||||
PGA3 | ENST00000539649.1 | n.153C>T | non_coding_transcript_exon_variant | Exon 2 of 3 | 2 |
Frequencies
GnomAD3 genomes Cov.: 16
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000316 AC: 4AN: 1267736Hom.: 0 Cov.: 26 AF XY: 0.00000157 AC XY: 1AN XY: 635080
GnomAD4 genome Cov.: 16
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.103C>T (p.R35C) alteration is located in exon 2 (coding exon 2) of the PGA3 gene. This alteration results from a C to T substitution at nucleotide position 103, causing the arginine (R) at amino acid position 35 to be replaced by a cysteine (C). 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