11-61204232-C-G
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001079807.4(PGA3):c.182C>G(p.Thr61Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000244 in 1,313,332 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/21 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 Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PGA3 | ENST00000325558.11 | c.182C>G | p.Thr61Ser | missense_variant | Exon 2 of 9 | 1 | NM_001079807.4 | ENSP00000322192.6 | ||
PGA3 | ENST00000535551.1 | n.926C>G | non_coding_transcript_exon_variant | Exon 1 of 3 | 3 | |||||
PGA3 | ENST00000537954.5 | n.232C>G | non_coding_transcript_exon_variant | Exon 2 of 2 | 2 | |||||
PGA3 | ENST00000539649.1 | n.232C>G | non_coding_transcript_exon_variant | Exon 2 of 3 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 3AN: 133208Hom.: 0 Cov.: 22 FAILED QC
GnomAD3 exomes AF: 0.0000394 AC: 9AN: 228494Hom.: 3 AF XY: 0.0000647 AC XY: 8AN XY: 123592
GnomAD4 exome AF: 0.0000244 AC: 32AN: 1313332Hom.: 7 Cov.: 30 AF XY: 0.0000229 AC XY: 15AN XY: 654434
GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000225 AC: 3AN: 133208Hom.: 0 Cov.: 22 AF XY: 0.0000308 AC XY: 2AN XY: 65008
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.182C>G (p.T61S) alteration is located in exon 2 (coding exon 2) of the PGA3 gene. This alteration results from a C to G substitution at nucleotide position 182, causing the threonine (T) at amino acid position 61 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