chr6-41744668-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_002630.4(PGC):c.200C>T(p.Ala67Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000533 in 1,613,952 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002630.4 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 | UniProt |
---|---|---|---|---|---|---|---|
PGC | NM_002630.4 | c.200C>T | p.Ala67Val | missense_variant | 2/9 | ENST00000373025.7 | |
PGC | NM_001166424.2 | c.200C>T | p.Ala67Val | missense_variant | 2/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PGC | ENST00000373025.7 | c.200C>T | p.Ala67Val | missense_variant | 2/9 | 1 | NM_002630.4 | P1 | |
PGC | ENST00000425343.6 | c.200C>T | p.Ala67Val | missense_variant | 2/7 | 2 | |||
PGC | ENST00000356667.8 | c.200C>T | p.Ala67Val | missense_variant | 2/4 | 5 | |||
PGC | ENST00000415707.1 | c.212C>T | p.Ala71Val | missense_variant | 2/3 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000723 AC: 11AN: 152144Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000358 AC: 9AN: 251346Hom.: 0 AF XY: 0.0000589 AC XY: 8AN XY: 135860
GnomAD4 exome AF: 0.0000513 AC: 75AN: 1461808Hom.: 0 Cov.: 32 AF XY: 0.0000674 AC XY: 49AN XY: 727220
GnomAD4 genome ? AF: 0.0000723 AC: 11AN: 152144Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74328
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 14, 2023 | The c.200C>T (p.A67V) alteration is located in exon 2 (coding exon 2) of the PGC gene. This alteration results from a C to T substitution at nucleotide position 200, causing the alanine (A) at amino acid position 67 to be replaced by a valine (V). 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