rs75993383
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_138477.4(CDAN1):c.2174+20G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00473 in 1,613,924 control chromosomes in the GnomAD database, including 197 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.022 ( 105 hom., cov: 33)
Exomes 𝑓: 0.0030 ( 92 hom. )
Consequence
CDAN1
NM_138477.4 intron
NM_138477.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.299
Genes affected
CDAN1 (HGNC:1713): (codanin 1) This gene encodes a protein that appears to play a role in nuclear envelope integrity, possibly related to microtubule attachments. Mutations in this gene cause congenital dyserythropoietic anemia type I, a disease resulting in morphological and functional abnormalities of erythropoiesis. [provided by RefSeq, Jul 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.79).
BP6
?
Variant 15-42730578-C-T is Benign according to our data. Variant chr15-42730578-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 262369.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.069 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CDAN1 | NM_138477.4 | c.2174+20G>A | intron_variant | ENST00000356231.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDAN1 | ENST00000356231.4 | c.2174+20G>A | intron_variant | 1 | NM_138477.4 | P1 | |||
CDAN1 | ENST00000562465.5 | c.167+20G>A | intron_variant, NMD_transcript_variant | 1 | |||||
CDAN1 | ENST00000643434.1 | c.*1352+20G>A | intron_variant, NMD_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0214 AC: 3262AN: 152208Hom.: 102 Cov.: 33
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GnomAD3 exomes AF: 0.00638 AC: 1599AN: 250794Hom.: 44 AF XY: 0.00498 AC XY: 676AN XY: 135770
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GnomAD4 exome AF: 0.00297 AC: 4339AN: 1461598Hom.: 92 Cov.: 34 AF XY: 0.00267 AC XY: 1940AN XY: 727108
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GnomAD4 genome ? AF: 0.0216 AC: 3292AN: 152326Hom.: 105 Cov.: 33 AF XY: 0.0206 AC XY: 1534AN XY: 74490
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 26, 2024 | - - |
Anemia, congenital dyserythropoietic, type 1a Benign:1
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Nov 03, 2023 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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