6-170583624-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_002598.4(PDCD2):c.407G>A(p.Arg136Lys) variant causes a missense change. The variant allele was found at a frequency of 0.0000564 in 1,614,036 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_002598.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000322 AC: 49AN: 152122Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.0000557 AC: 14AN: 251412Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135882
GnomAD4 exome AF: 0.0000280 AC: 41AN: 1461796Hom.: 0 Cov.: 32 AF XY: 0.0000151 AC XY: 11AN XY: 727200
GnomAD4 genome AF: 0.000328 AC: 50AN: 152240Hom.: 1 Cov.: 32 AF XY: 0.000309 AC XY: 23AN XY: 74430
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.407G>A (p.R136K) alteration is located in exon 2 (coding exon 2) of the PDCD2 gene. This alteration results from a G to A substitution at nucleotide position 407, causing the arginine (R) at amino acid position 136 to be replaced by a lysine (K). 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