X-70427167-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_017711.4(GDPD2):c.733C>T(p.Arg245Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000498 in 1,205,115 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 4 hemizygotes in GnomAD. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_017711.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000180 AC: 2AN: 111281Hom.: 0 Cov.: 23 AF XY: 0.0000299 AC XY: 1AN XY: 33481
GnomAD3 exomes AF: 0.00000545 AC: 1AN: 183349Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 67783
GnomAD4 exome AF: 0.00000366 AC: 4AN: 1093834Hom.: 0 Cov.: 30 AF XY: 0.00000835 AC XY: 3AN XY: 359368
GnomAD4 genome AF: 0.0000180 AC: 2AN: 111281Hom.: 0 Cov.: 23 AF XY: 0.0000299 AC XY: 1AN XY: 33481
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.733C>T (p.R245W) alteration is located in exon 9 (coding exon 8) of the GDPD2 gene. This alteration results from a C to T substitution at nucleotide position 733, causing the arginine (R) at amino acid position 245 to be replaced by a tryptophan (W). 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