rs114779238
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_138477.4(CDAN1):c.2836C>T(p.Arg946Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00257 in 1,613,816 control chromosomes in the GnomAD database, including 59 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R946Q) 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.2836C>T | p.Arg946Trp | missense_variant | 21/28 | ENST00000356231.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDAN1 | ENST00000356231.4 | c.2836C>T | p.Arg946Trp | missense_variant | 21/28 | 1 | NM_138477.4 | P1 | |
CDAN1 | ENST00000562465.5 | c.829C>T | p.Arg277Trp | missense_variant, NMD_transcript_variant | 8/15 | 1 | |||
CDAN1 | ENST00000643434.1 | c.*2014C>T | 3_prime_UTR_variant, NMD_transcript_variant | 19/25 |
Frequencies
GnomAD3 genomes AF: 0.0116 AC: 1768AN: 152144Hom.: 26 Cov.: 32
GnomAD3 exomes AF: 0.00398 AC: 999AN: 250836Hom.: 14 AF XY: 0.00324 AC XY: 439AN XY: 135702
GnomAD4 exome AF: 0.00162 AC: 2366AN: 1461554Hom.: 33 Cov.: 32 AF XY: 0.00153 AC XY: 1115AN XY: 727082
GnomAD4 genome AF: 0.0117 AC: 1775AN: 152262Hom.: 26 Cov.: 32 AF XY: 0.0117 AC XY: 872AN XY: 74438
ClinVar
Submissions by phenotype
not provided Benign:3
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 16, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Aug 24, 2015 | - - |
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Mar 01, 2022 | CDAN1: BS1, BS2 - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Congenital dyserythropoietic anemia, type I Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Apr 27, 2017 | This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. - |
Anemia, congenital dyserythropoietic, type 1a Benign:1
Likely benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | May 25, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at