GeneBe

rs80338694

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7

The NM_138477.4(CDAN1):​c.156C>T​(p.Phe52Phe) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

CDAN1
NM_138477.4 synonymous

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.10

Publications

6 publications found
Variant links:
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]
CDAN1 Gene-Disease associations (from GenCC):
  • anemia, congenital dyserythropoietic, type 1a
    Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics
  • congenital dyserythropoietic anemia type 1
    Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
  • congenital dyserythropoietic anemia
    Inheritance: AR Classification: LIMITED Submitted by: Genomics England PanelApp

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -3 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.56).
BP7
Synonymous conserved (PhyloP=1.1 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_138477.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
CDAN1
NM_138477.4
MANE Select
c.156C>Tp.Phe52Phe
synonymous
Exon 2 of 28NP_612486.2

Ensembl Transcripts

Selected
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
CDAN1
ENST00000356231.4
TSL:1 MANE Select
c.156C>Tp.Phe52Phe
synonymous
Exon 2 of 28ENSP00000348564.3
CDAN1
ENST00000563260.1
TSL:3
c.132C>Tp.Phe44Phe
synonymous
Exon 2 of 2ENSP00000455536.1
CDAN1
ENST00000643434.1
n.90+298C>T
intron
N/AENSP00000494699.1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD2 exomes
AF:
0.00
AC:
0
AN:
169766
AF XY:
0.00
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
1408716
Hom.:
0
Cov.:
33
AF XY:
0.00
AC XY:
0
AN XY:
698320
African (AFR)
AF:
0.00
AC:
0
AN:
29634
American (AMR)
AF:
0.00
AC:
0
AN:
38110
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
24508
East Asian (EAS)
AF:
0.00
AC:
0
AN:
34850
South Asian (SAS)
AF:
0.00
AC:
0
AN:
79420
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
49130
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
5656
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
1089192
Other (OTH)
AF:
0.00
AC:
0
AN:
58216
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.56
CADD
Benign
14
DANN
Benign
0.94
PhyloP100
1.1
PromoterAI
-0.017
Neutral

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.070
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs80338694; hg19: chr15-43028913; API