2-206304824-A-T
Variant names:
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_020923.3(ZDBF2):c.296A>T(p.Asp99Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0013 in 1,613,726 control chromosomes in the GnomAD database, including 10 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 Benign (★).
Frequency
Genomes: 𝑓 0.0011 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0013 ( 10 hom. )
Consequence
ZDBF2
NM_020923.3 missense
NM_020923.3 missense
Scores
1
17
Clinical Significance
Conservation
PhyloP100: -0.250
Genes affected
ZDBF2 (HGNC:29313): (zinc finger DBF-type containing 2) This gene encodes a protein containing DBF4-type zinc finger domains. This gene is imprinted and paternally expressed in lymphocytes but is more stochastically expressed in the placenta. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2015]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.005754411).
BP6
Variant 2-206304824-A-T is Benign according to our data. Variant chr2-206304824-A-T is described in ClinVar as [Benign]. Clinvar id is 2823821.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High Homozygotes in GnomAdExome4 at 10 AR gene
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00106 AC: 161AN: 152074Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.00175 AC: 435AN: 249022Hom.: 3 AF XY: 0.00208 AC XY: 281AN XY: 135086
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GnomAD4 exome AF: 0.00132 AC: 1932AN: 1461534Hom.: 10 Cov.: 30 AF XY: 0.00152 AC XY: 1106AN XY: 727036
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GnomAD4 genome AF: 0.00106 AC: 161AN: 152192Hom.: 0 Cov.: 32 AF XY: 0.00102 AC XY: 76AN XY: 74408
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Oct 17, 2024
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
DEOGEN2
Benign
T;T;.;.;.;.;.;T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
M_CAP
Benign
T
MetaRNN
Benign
T;T;T;T;T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
N;N;.;.;.;.;.;.
PrimateAI
Benign
T
PROVEAN
Benign
N;.;.;.;.;.;.;.
REVEL
Benign
Sift
Benign
T;.;.;.;.;.;.;.
Sift4G
Uncertain
D;.;.;.;.;.;.;D
Polyphen
P;P;.;.;.;.;.;.
Vest4
MVP
MPC
ClinPred
T
GERP RS
Varity_R
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