2-206304824-A-T

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

Scores

1
17

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.250
Variant links:
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]

Genome browser will be placed here

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

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ZDBF2NM_020923.3 linkc.296A>T p.Asp99Val missense_variant Exon 5 of 5 ENST00000374423.9 NP_065974.1 Q9HCK1N0DVB2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ZDBF2ENST00000374423.9 linkc.296A>T p.Asp99Val missense_variant Exon 5 of 5 1 NM_020923.3 ENSP00000363545.3 Q9HCK1

Frequencies

GnomAD3 genomes
AF:
0.00106
AC:
161
AN:
152074
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.000290
Gnomad AMI
AF:
0.00987
Gnomad AMR
AF:
0.00118
Gnomad ASJ
AF:
0.000576
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00519
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00949
Gnomad NFE
AF:
0.00125
Gnomad OTH
AF:
0.00335
GnomAD3 exomes
AF:
0.00175
AC:
435
AN:
249022
Hom.:
3
AF XY:
0.00208
AC XY:
281
AN XY:
135086
show subpopulations
Gnomad AFR exome
AF:
0.000129
Gnomad AMR exome
AF:
0.00102
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00690
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00156
Gnomad OTH exome
AF:
0.00182
GnomAD4 exome
AF:
0.00132
AC:
1932
AN:
1461534
Hom.:
10
Cov.:
30
AF XY:
0.00152
AC XY:
1106
AN XY:
727036
show subpopulations
Gnomad4 AFR exome
AF:
0.0000896
Gnomad4 AMR exome
AF:
0.00110
Gnomad4 ASJ exome
AF:
0.0000383
Gnomad4 EAS exome
AF:
0.0000252
Gnomad4 SAS exome
AF:
0.00748
Gnomad4 FIN exome
AF:
0.0000375
Gnomad4 NFE exome
AF:
0.000971
Gnomad4 OTH exome
AF:
0.00149
GnomAD4 genome
AF:
0.00106
AC:
161
AN:
152192
Hom.:
0
Cov.:
32
AF XY:
0.00102
AC XY:
76
AN XY:
74408
show subpopulations
Gnomad4 AFR
AF:
0.000289
Gnomad4 AMR
AF:
0.00118
Gnomad4 ASJ
AF:
0.000576
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00519
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00125
Gnomad4 OTH
AF:
0.00331
Alfa
AF:
0.00157
Hom.:
2
Bravo
AF:
0.00106
TwinsUK
AF:
0.00
AC:
0
ALSPAC
AF:
0.000259
AC:
1
ESP6500AA
AF:
0.00
AC:
0
ESP6500EA
AF:
0.00132
AC:
11
ExAC
AF:
0.00182
AC:
220
Asia WGS
AF:
0.00144
AC:
5
AN:
3478
EpiCase
AF:
0.00289
EpiControl
AF:
0.00243

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: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.10
BayesDel_addAF
Benign
-0.54
T
BayesDel_noAF
Benign
-0.55
CADD
Benign
5.1
DANN
Benign
0.76
DEOGEN2
Benign
0.017
T;T;.;.;.;.;.;T
Eigen
Benign
-0.83
Eigen_PC
Benign
-0.97
FATHMM_MKL
Benign
0.37
N
M_CAP
Benign
0.0015
T
MetaRNN
Benign
0.0058
T;T;T;T;T;T;T;T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
0.69
N;N;.;.;.;.;.;.
PrimateAI
Benign
0.26
T
PROVEAN
Benign
-1.6
N;.;.;.;.;.;.;.
REVEL
Benign
0.059
Sift
Benign
0.085
T;.;.;.;.;.;.;.
Sift4G
Uncertain
0.033
D;.;.;.;.;.;.;D
Polyphen
0.65
P;P;.;.;.;.;.;.
Vest4
0.21
MVP
0.21
MPC
0.34
ClinPred
0.035
T
GERP RS
1.5
Varity_R
0.11
gMVP
0.040

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs149317779; hg19: chr2-207169548; API