chr20-5598750-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_019593.5(GPCPD1):c.121C>A(p.Leu41Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000652 in 1,609,994 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_019593.5 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 |
---|---|---|---|---|---|---|---|
GPCPD1 | NM_019593.5 | c.121C>A | p.Leu41Ile | missense_variant | 3/20 | ENST00000379019.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GPCPD1 | ENST00000379019.7 | c.121C>A | p.Leu41Ile | missense_variant | 3/20 | 1 | NM_019593.5 | P1 | |
GPCPD1 | ENST00000481690.2 | c.121C>A | p.Leu41Ile | missense_variant, NMD_transcript_variant | 3/8 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152116Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 251330Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135836
GnomAD4 exome AF: 0.0000686 AC: 100AN: 1457878Hom.: 0 Cov.: 28 AF XY: 0.0000634 AC XY: 46AN XY: 725610
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152116Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74294
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 27, 2023 | The c.121C>A (p.L41I) alteration is located in exon 3 (coding exon 2) of the GPCPD1 gene. This alteration results from a C to A substitution at nucleotide position 121, causing the leucine (L) at amino acid position 41 to be replaced by an isoleucine (I). 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