chrX-45151862-C-T
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_176819.4(DIPK2B):c.1092G>A(p.Lys364Lys) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000788 in 1,210,112 control chromosomes in the GnomAD database, including 3 homozygotes. There are 248 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_176819.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -17 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DIPK2B | NM_176819.4 | c.1092G>A | p.Lys364Lys | synonymous_variant | Exon 5 of 5 | ENST00000398000.7 | NP_789789.2 | |
DIPK2B | XM_005272670.1 | c.918G>A | p.Lys306Lys | synonymous_variant | Exon 4 of 4 | XP_005272727.1 | ||
DIPK2B | XM_006724559.1 | c.840G>A | p.Lys280Lys | synonymous_variant | Exon 4 of 4 | XP_006724622.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00374 AC: 422AN: 112729Hom.: 2 Cov.: 24 AF XY: 0.00347 AC XY: 121AN XY: 34871
GnomAD3 exomes AF: 0.000915 AC: 163AN: 178099Hom.: 0 AF XY: 0.000618 AC XY: 40AN XY: 64687
GnomAD4 exome AF: 0.000481 AC: 528AN: 1097330Hom.: 1 Cov.: 31 AF XY: 0.000345 AC XY: 125AN XY: 362802
GnomAD4 genome AF: 0.00377 AC: 425AN: 112782Hom.: 2 Cov.: 24 AF XY: 0.00352 AC XY: 123AN XY: 34934
ClinVar
Submissions by phenotype
not provided Benign:2
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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