2-206304852-C-T
Variant names:
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_020923.3(ZDBF2):c.324C>T(p.Ser108Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000397 in 1,613,602 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00011 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000032 ( 1 hom. )
Consequence
ZDBF2
NM_020923.3 synonymous
NM_020923.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.482
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 Likely_benign. Variant got -5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.74).
BP6
Variant 2-206304852-C-T is Benign according to our data. Variant chr2-206304852-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2710896.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.482 with no splicing effect.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000112 AC: 17AN: 151968Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000763 AC: 19AN: 248988Hom.: 0 AF XY: 0.0000592 AC XY: 8AN XY: 135092
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GnomAD4 exome AF: 0.0000322 AC: 47AN: 1461516Hom.: 1 Cov.: 30 AF XY: 0.0000413 AC XY: 30AN XY: 727050
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GnomAD4 genome AF: 0.000112 AC: 17AN: 152086Hom.: 0 Cov.: 32 AF XY: 0.000161 AC XY: 12AN XY: 74356
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Oct 04, 2023
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
- -
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at