20-5558033-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_019593.5(GPCPD1):c.1741G>A(p.Val581Ile) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000626 in 1,597,202 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts 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
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GPCPD1 | ENST00000379019.7 | c.1741G>A | p.Val581Ile | missense_variant | Exon 19 of 20 | 1 | NM_019593.5 | ENSP00000368305.4 | ||
GPCPD1 | ENST00000418646.5 | c.514G>A | p.Val172Ile | missense_variant | Exon 6 of 7 | 5 | ENSP00000396720.1 | |||
GPCPD1 | ENST00000481038.5 | n.3149G>A | non_coding_transcript_exon_variant | Exon 14 of 15 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000243 AC: 37AN: 152128Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000677 AC: 17AN: 251068Hom.: 0 AF XY: 0.0000811 AC XY: 11AN XY: 135708
GnomAD4 exome AF: 0.0000436 AC: 63AN: 1444956Hom.: 1 Cov.: 25 AF XY: 0.0000347 AC XY: 25AN XY: 719994
GnomAD4 genome AF: 0.000243 AC: 37AN: 152246Hom.: 0 Cov.: 32 AF XY: 0.000228 AC XY: 17AN XY: 74444
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1741G>A (p.V581I) alteration is located in exon 19 (coding exon 18) of the GPCPD1 gene. This alteration results from a G to A substitution at nucleotide position 1741, causing the valine (V) at amino acid position 581 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