rs782144704
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 4P and 4B. PM1PP3_ModerateBS2
The NM_001029891.3(PGAM4):c.41G>A(p.Ser14Asn) variant causes a missense change. The variant allele was found at a frequency of 0.00000496 in 1,210,538 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 3 hemizygotes in GnomAD. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001029891.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PGAM4 | NM_001029891.3 | c.41G>A | p.Ser14Asn | missense_variant | Exon 1 of 1 | ENST00000458128.3 | NP_001025062.1 | |
ATP7A | NM_000052.7 | c.-21-2023C>T | intron_variant | Intron 1 of 22 | ENST00000341514.11 | NP_000043.4 | ||
ATP7A | NM_001282224.2 | c.-21-2023C>T | intron_variant | Intron 1 of 21 | NP_001269153.1 | |||
ATP7A | NR_104109.2 | n.144-2023C>T | intron_variant | Intron 1 of 9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PGAM4 | ENST00000458128.3 | c.41G>A | p.Ser14Asn | missense_variant | Exon 1 of 1 | 6 | NM_001029891.3 | ENSP00000412189.1 | ||
ATP7A | ENST00000341514.11 | c.-21-2023C>T | intron_variant | Intron 1 of 22 | 1 | NM_000052.7 | ENSP00000345728.6 |
Frequencies
GnomAD3 genomes AF: 0.00000889 AC: 1AN: 112497Hom.: 0 Cov.: 23 AF XY: 0.0000289 AC XY: 1AN XY: 34645
GnomAD3 exomes AF: 0.0000164 AC: 3AN: 183227Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 67773
GnomAD4 exome AF: 0.00000455 AC: 5AN: 1098041Hom.: 0 Cov.: 33 AF XY: 0.00000550 AC XY: 2AN XY: 363453
GnomAD4 genome AF: 0.00000889 AC: 1AN: 112497Hom.: 0 Cov.: 23 AF XY: 0.0000289 AC XY: 1AN XY: 34645
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.41G>A (p.S14N) alteration is located in exon 1 (coding exon 1) of the PGAM4 gene. This alteration results from a G to A substitution at nucleotide position 41, causing the serine (S) at amino acid position 14 to be replaced by an asparagine (N). 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