X-45191851-G-T
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_176819.4(DIPK2B):c.398C>A(p.Ala133Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00337 in 1,210,567 control chromosomes in the GnomAD database, including 89 homozygotes. There are 1,101 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.017 ( 44 hom., 540 hem., cov: 24)
Exomes 𝑓: 0.0019 ( 45 hom. 561 hem. )
Consequence
DIPK2B
NM_176819.4 missense
NM_176819.4 missense
Scores
3
10
Clinical Significance
Conservation
PhyloP100: 0.750
Genes affected
DIPK2B (HGNC:25866): (divergent protein kinase domain 2B) Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Apr 2022]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.0016578138).
BP6
Variant X-45191851-G-T is Benign according to our data. Variant chrX-45191851-G-T is described in ClinVar as [Benign]. Clinvar id is 718331.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.058 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DIPK2B | NM_176819.4 | c.398C>A | p.Ala133Glu | missense_variant | 2/5 | ENST00000398000.7 | NP_789789.2 | |
DIPK2B | NM_024689.3 | c.398C>A | p.Ala133Glu | missense_variant | 2/3 | NP_078965.2 | ||
DIPK2B | XM_005272670.1 | c.398C>A | p.Ala133Glu | missense_variant | 2/4 | XP_005272727.1 | ||
DIPK2B | XM_006724559.1 | c.398C>A | p.Ala133Glu | missense_variant | 2/4 | XP_006724622.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0174 AC: 1951AN: 112396Hom.: 44 Cov.: 24 AF XY: 0.0153 AC XY: 530AN XY: 34556
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GnomAD3 exomes AF: 0.00517 AC: 947AN: 183320Hom.: 17 AF XY: 0.00335 AC XY: 227AN XY: 67772
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GnomAD4 exome AF: 0.00193 AC: 2120AN: 1098117Hom.: 45 Cov.: 33 AF XY: 0.00154 AC XY: 561AN XY: 363471
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GnomAD4 genome AF: 0.0175 AC: 1963AN: 112450Hom.: 44 Cov.: 24 AF XY: 0.0156 AC XY: 540AN XY: 34620
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Apr 20, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
FATHMM_MKL
Benign
N
LIST_S2
Benign
T;T
MetaRNN
Benign
T;T
MetaSVM
Benign
T
PROVEAN
Benign
N;D
REVEL
Benign
Sift
Uncertain
D;D
Sift4G
Uncertain
D;D
Vest4
MVP
MPC
ClinPred
T
GERP RS
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at