X-77969275-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001029891.3(PGAM4):c.364C>T(p.Pro122Ser) variant causes a missense change. The variant allele was found at a frequency of 0.00000579 in 1,209,754 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 2 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001029891.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PGAM4 | NM_001029891.3 | c.364C>T | p.Pro122Ser | missense_variant | Exon 1 of 1 | ENST00000458128.3 | NP_001025062.1 | |
ATP7A | NM_000052.7 | c.-21-2346G>A | intron_variant | Intron 1 of 22 | ENST00000341514.11 | NP_000043.4 | ||
ATP7A | NM_001282224.2 | c.-21-2346G>A | intron_variant | Intron 1 of 21 | NP_001269153.1 | |||
ATP7A | NR_104109.2 | n.144-2346G>A | intron_variant | Intron 1 of 9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PGAM4 | ENST00000458128.3 | c.364C>T | p.Pro122Ser | missense_variant | Exon 1 of 1 | 6 | NM_001029891.3 | ENSP00000412189.1 | ||
ATP7A | ENST00000341514.11 | c.-21-2346G>A | intron_variant | Intron 1 of 22 | 1 | NM_000052.7 | ENSP00000345728.6 |
Frequencies
GnomAD3 genomes AF: 0.0000179 AC: 2AN: 111651Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 33897
GnomAD3 exomes AF: 0.0000222 AC: 4AN: 180568Hom.: 0 AF XY: 0.0000150 AC XY: 1AN XY: 66798
GnomAD4 exome AF: 0.00000455 AC: 5AN: 1098052Hom.: 0 Cov.: 32 AF XY: 0.00000550 AC XY: 2AN XY: 363468
GnomAD4 genome AF: 0.0000179 AC: 2AN: 111702Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 33958
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.364C>T (p.P122S) alteration is located in exon 1 (coding exon 1) of the PGAM4 gene. This alteration results from a C to T substitution at nucleotide position 364, causing the proline (P) at amino acid position 122 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