11-77227914-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_182833.3(GDPD4):c.1475G>A(p.Arg492Gln) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000192 in 1,610,948 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/23 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_182833.3 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GDPD4 | NM_182833.3 | c.1475G>A | p.Arg492Gln | missense_variant, splice_region_variant | Exon 16 of 17 | ENST00000315938.5 | NP_878253.1 | |
GDPD4 | XM_011544834.1 | c.1553G>A | p.Arg518Gln | missense_variant, splice_region_variant | Exon 16 of 18 | XP_011543136.1 | ||
GDPD4 | XM_047426557.1 | c.881G>A | p.Arg294Gln | missense_variant, splice_region_variant | Exon 12 of 13 | XP_047282513.1 | ||
GDPD4 | XM_047426558.1 | c.881G>A | p.Arg294Gln | missense_variant, splice_region_variant | Exon 12 of 13 | XP_047282514.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GDPD4 | ENST00000315938.5 | c.1475G>A | p.Arg492Gln | missense_variant, splice_region_variant | Exon 16 of 17 | 1 | NM_182833.3 | ENSP00000320815.4 | ||
GDPD4 | ENST00000376217.6 | c.1475G>A | p.Arg492Gln | missense_variant, splice_region_variant | Exon 15 of 17 | 1 | ENSP00000365390.2 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152180Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 251326Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135840
GnomAD4 exome AF: 0.0000171 AC: 25AN: 1458768Hom.: 0 Cov.: 30 AF XY: 0.0000124 AC XY: 9AN XY: 725918
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152180Hom.: 0 Cov.: 31 AF XY: 0.0000403 AC XY: 3AN XY: 74352
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1475G>A (p.R492Q) alteration is located in exon 15 (coding exon 14) of the GDPD4 gene. This alteration results from a G to A substitution at nucleotide position 1475, causing the arginine (R) at amino acid position 492 to be replaced by a glutamine (Q). 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