15-42728785-G-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_138477.4(CDAN1):c.2671C>T(p.Arg891Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.207 in 1,613,806 control chromosomes in the GnomAD database, including 39,195 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R891H) has been classified as Uncertain significance.
Frequency
Consequence
NM_138477.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CDAN1 | NM_138477.4 | c.2671C>T | p.Arg891Cys | missense_variant | 20/28 | ENST00000356231.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDAN1 | ENST00000356231.4 | c.2671C>T | p.Arg891Cys | missense_variant | 20/28 | 1 | NM_138477.4 | P1 | |
CDAN1 | ENST00000562465.5 | c.664C>T | p.Arg222Cys | missense_variant, NMD_transcript_variant | 7/15 | 1 | |||
CDAN1 | ENST00000643434.1 | c.*1849C>T | 3_prime_UTR_variant, NMD_transcript_variant | 18/25 |
Frequencies
GnomAD3 genomes AF: 0.255 AC: 38742AN: 151990Hom.: 6043 Cov.: 32
GnomAD3 exomes AF: 0.208 AC: 52115AN: 251126Hom.: 6661 AF XY: 0.214 AC XY: 29088AN XY: 135760
GnomAD4 exome AF: 0.202 AC: 295429AN: 1461698Hom.: 33145 Cov.: 39 AF XY: 0.207 AC XY: 150275AN XY: 727158
GnomAD4 genome AF: 0.255 AC: 38778AN: 152108Hom.: 6050 Cov.: 32 AF XY: 0.255 AC XY: 18945AN XY: 74376
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 04, 2021 | This variant is associated with the following publications: (PMID: 29031773) - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Congenital dyserythropoietic anemia, type I Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 12, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
Anemia, congenital dyserythropoietic, type 1a Benign:1
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Nov 30, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at