rs384828
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_173543.3(DZIP1L):c.1288+118T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.689 in 1,071,740 control chromosomes in the GnomAD database, including 256,523 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.65 ( 32468 hom., cov: 32)
Exomes 𝑓: 0.70 ( 224055 hom. )
Consequence
DZIP1L
NM_173543.3 intron
NM_173543.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0260
Genes affected
DZIP1L (HGNC:26551): (DAZ interacting zinc finger protein 1 like) Predicted to enable metal ion binding activity. Involved in cilium assembly and regulation of protein localization. Located in ciliary basal body. Colocalizes with centriole. Implicated in polycystic kidney disease 5. [provided by Alliance of Genome Resources, Apr 2022]
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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=-0.95).
BP6
?
Variant 3-138080449-A-T is Benign according to our data. Variant chr3-138080449-A-T is described in ClinVar as [Benign]. Clinvar id is 1271645.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.698 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DZIP1L | NM_173543.3 | c.1288+118T>A | intron_variant | ENST00000327532.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DZIP1L | ENST00000327532.7 | c.1288+118T>A | intron_variant | 1 | NM_173543.3 | P2 | |||
DZIP1L | ENST00000469243.5 | c.1288+118T>A | intron_variant | 2 | A2 | ||||
DZIP1L | ENST00000466301.1 | n.268T>A | non_coding_transcript_exon_variant | 2/2 | 3 | ||||
DZIP1L | ENST00000488595.1 | n.360+118T>A | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.649 AC: 98586AN: 151952Hom.: 32451 Cov.: 32
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GnomAD4 exome AF: 0.696 AC: 639870AN: 919670Hom.: 224055 Cov.: 11 AF XY: 0.695 AC XY: 326257AN XY: 469176
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GnomAD4 genome ? AF: 0.649 AC: 98653AN: 152070Hom.: 32468 Cov.: 32 AF XY: 0.645 AC XY: 47961AN XY: 74336
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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 11, 2021 | - - |
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