chrX-70429557-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_017711.4(GDPD2):c.1001C>T(p.Thr334Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0001 in 1,206,906 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 33 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. 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 Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000107 AC: 12AN: 111801Hom.: 0 Cov.: 22 AF XY: 0.0000294 AC XY: 1AN XY: 33971
GnomAD3 exomes AF: 0.000186 AC: 34AN: 183091Hom.: 0 AF XY: 0.000192 AC XY: 13AN XY: 67575
GnomAD4 exome AF: 0.0000995 AC: 109AN: 1095051Hom.: 0 Cov.: 30 AF XY: 0.0000888 AC XY: 32AN XY: 360523
GnomAD4 genome AF: 0.000107 AC: 12AN: 111855Hom.: 0 Cov.: 22 AF XY: 0.0000294 AC XY: 1AN XY: 34035
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1001C>T (p.T334M) alteration is located in exon 11 (coding exon 10) of the GDPD2 gene. This alteration results from a C to T substitution at nucleotide position 1001, causing the threonine (T) at amino acid position 334 to be replaced by a methionine (M). 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