6-73353369-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001025290.3(DPPA5):c.302A>G(p.Lys101Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000452 in 1,614,100 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. K101Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_001025290.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000243 AC: 37AN: 152098Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000187 AC: 47AN: 251494Hom.: 0 AF XY: 0.000154 AC XY: 21AN XY: 135922
GnomAD4 exome AF: 0.000473 AC: 692AN: 1461884Hom.: 1 Cov.: 31 AF XY: 0.000441 AC XY: 321AN XY: 727242
GnomAD4 genome AF: 0.000243 AC: 37AN: 152216Hom.: 0 Cov.: 32 AF XY: 0.000228 AC XY: 17AN XY: 74424
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.302A>G (p.K101R) alteration is located in exon 3 (coding exon 3) of the DPPA5 gene. This alteration results from a A to G substitution at nucleotide position 302, causing the lysine (K) at amino acid position 101 to be replaced by an arginine (R). 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