X-45191821-C-A
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_176819.4(DIPK2B):c.428G>T(p.Arg143Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00116 in 1,210,636 control chromosomes in the GnomAD database, including 17 homozygotes. There are 391 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Consequence
NM_176819.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DIPK2B | NM_176819.4 | c.428G>T | p.Arg143Leu | missense_variant | Exon 2 of 5 | ENST00000398000.7 | NP_789789.2 | |
DIPK2B | NM_024689.3 | c.428G>T | p.Arg143Leu | missense_variant | Exon 2 of 3 | NP_078965.2 | ||
DIPK2B | XM_005272670.1 | c.428G>T | p.Arg143Leu | missense_variant | Exon 2 of 4 | XP_005272727.1 | ||
DIPK2B | XM_006724559.1 | c.428G>T | p.Arg143Leu | missense_variant | Exon 2 of 4 | XP_006724622.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00154 AC: 173AN: 112534Hom.: 3 Cov.: 23 AF XY: 0.00118 AC XY: 41AN XY: 34680
GnomAD3 exomes AF: 0.00493 AC: 903AN: 183149Hom.: 11 AF XY: 0.00349 AC XY: 236AN XY: 67619
GnomAD4 exome AF: 0.00112 AC: 1229AN: 1098049Hom.: 14 Cov.: 33 AF XY: 0.000958 AC XY: 348AN XY: 363405
GnomAD4 genome AF: 0.00155 AC: 174AN: 112587Hom.: 3 Cov.: 23 AF XY: 0.00124 AC XY: 43AN XY: 34743
ClinVar
Submissions by phenotype
DIPK2B-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at