rs2292155
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001379286.1(ZNF423):c.101-66G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.364 in 1,551,884 control chromosomes in the GnomAD database, including 105,593 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.39 ( 11717 hom., cov: 32)
Exomes 𝑓: 0.36 ( 93876 hom. )
Consequence
ZNF423
NM_001379286.1 intron
NM_001379286.1 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.15
Genes affected
ZNF423 (HGNC:16762): (zinc finger protein 423) The protein encoded by this gene is a nuclear protein that belongs to the family of Kruppel-like C2H2 zinc finger proteins. It functions as a DNA-binding transcription factor by using distinct zinc fingers in different signaling pathways. Thus, it is thought that this gene may have multiple roles in signal transduction during development. Mutations in this gene are associated with nephronophthisis-14 and Joubert syndrome-19. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2012]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.79).
BP6
?
Variant 16-49731037-C-T is Benign according to our data. Variant chr16-49731037-C-T is described in ClinVar as [Benign]. Clinvar id is 1239696.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.48 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZNF423 | NM_001379286.1 | c.101-66G>A | intron_variant | ENST00000563137.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF423 | ENST00000563137.7 | c.101-66G>A | intron_variant | 5 | NM_001379286.1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.386 AC: 58601AN: 151914Hom.: 11702 Cov.: 32
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GnomAD4 exome AF: 0.362 AC: 506790AN: 1399852Hom.: 93876 AF XY: 0.359 AC XY: 250181AN XY: 696176
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GnomAD4 genome ? AF: 0.386 AC: 58647AN: 152032Hom.: 11717 Cov.: 32 AF XY: 0.383 AC XY: 28480AN XY: 74282
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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
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 17, 2021 | - - |
Computational scores
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Benign
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Dann
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at