rs61747153

Variant names:

Your query was ambiguous. Multiple possible variants found:

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_138477.4(CDAN1):c.1969G>A(p.Gly657Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0146 in 1,614,064 control chromosomes in the GnomAD database, including 1,187 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.052 ( 554 hom., cov: 32)

Exomes 𝑓: 0.011 ( 633 hom. )

Consequence

CDAN1
NM_138477.4 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:6

Conservation

PhyloP100: 2.49

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: Ambry Genetics, ClinGen, Labcorp Genetics (formerly Invitae)
congenital dyserythropoietic anemia type 1
Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
congenital dyserythropoietic anemia
Inheritance: AR Classification: LIMITED Submitted by: Genomics England PanelApp

CDAN1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0014235973).

BP6

Variant 15-42730963-C-T is Benign according to our data. Variant chr15-42730963-C-T is described in ClinVar as Benign. ClinVar VariationId is 262368.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.159 is higher than 0.05.

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CDAN1	NM_138477.4	MANE Select	c.1969G>A	p.Gly657Ser	missense	Exon 13 of 28	NP_612486.2	Q8IWY9-2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
CDAN1	ENST00000356231.4	TSL:1 MANE Select	c.1969G>A	p.Gly657Ser	missense	Exon 13 of 28	ENSP00000348564.3	Q8IWY9-2
CDAN1	ENST00000913682.1		c.1972G>A	p.Gly658Ser	missense	Exon 13 of 28	ENSP00000583741.1
CDAN1	ENST00000913683.1		c.1969G>A	p.Gly657Ser	missense	Exon 13 of 28	ENSP00000583742.1

Frequencies

GnomAD3 genomes

AF:

0.0517

AC:

7864

AN:

152116

Hom.:

553

Cov.:

show subpopulations

Gnomad AFR

AF:

0.163

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0226

Gnomad ASJ

AF:

0.00144

Gnomad EAS

AF:

0.0573

Gnomad SAS

AF:

0.0189

Gnomad FIN

AF:

0.000377

Gnomad MID

AF:

0.0127

Gnomad NFE

AF:

0.00448

Gnomad OTH

AF:

0.0396

GnomAD2 exomes

AF:

0.0214

AC:

5373

AN:

251260

AF XY:

0.0188

show subpopulations

Gnomad AFR exome

AF:

0.169

Gnomad AMR exome

AF:

0.00954

Gnomad ASJ exome

AF:

0.00367

Gnomad EAS exome

AF:

0.0638

Gnomad FIN exome

AF:

0.000370

Gnomad NFE exome

AF:

0.00437

Gnomad OTH exome

AF:

0.0112

GnomAD4 exome

AF:

0.0107

AC:

15665

AN:

1461830

Hom.:

633

Cov.:

AF XY:

0.0106

AC XY:

7717

AN XY:

727214

show subpopulations

African (AFR)

AF:

0.171

AC:

5709

AN:

33478

American (AMR)

AF:

0.0112

AC:

500

AN:

44724

Ashkenazi Jewish (ASJ)

AF:

0.00230

AC:

AN:

26136

East Asian (EAS)

AF:

0.0505

AC:

2003

AN:

39698

South Asian (SAS)

AF:

0.0189

AC:

1630

AN:

86256

European-Finnish (FIN)

AF:

0.000374

AC:

AN:

53420

Middle Eastern (MID)

AF:

0.0109

AC:

AN:

5768

European-Non Finnish (NFE)

AF:

0.00419

AC:

4664

AN:

1111954

Other (OTH)

AF:

0.0168

AC:

1016

AN:

60396

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.482

Heterozygous variant carriers

1013

2026

3040

4053

5066

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

306

612

918

1224

1530

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0517

AC:

7878

AN:

152234

Hom.:

554

Cov.:

AF XY:

0.0505

AC XY:

3761

AN XY:

74412

show subpopulations

African (AFR)

AF:

0.162

AC:

6742

AN:

41524

American (AMR)

AF:

0.0226

AC:

345

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.00144

AC:

AN:

3470

East Asian (EAS)

AF:

0.0575

AC:

297

AN:

5168

South Asian (SAS)

AF:

0.0191

AC:

AN:

4822

European-Finnish (FIN)

AF:

0.000377

AC:

AN:

10600

Middle Eastern (MID)

AF:

0.0170

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00447

AC:

304

AN:

68030

Other (OTH)

AF:

0.0397

AC:

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

348

697

1045

1394

1742

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

164

246

328

410

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0237

Hom.:

158

Bravo

AF:

0.0603

TwinsUK

AF:

0.00351

AC:

ALSPAC

AF:

0.00389

AC:

ESP6500AA

AF:

0.160

AC:

707

ESP6500EA

AF:

0.00430

AC:

ExAC

AF:

0.0244

AC:

2959

Asia WGS

AF:

0.0430

AC:

149

AN:

3478

EpiCase

AF:

0.00447

EpiControl

AF:

0.00379

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (3)

Anemia, congenital dyserythropoietic, type 1a (1)

Congenital dyserythropoietic anemia, type I (1)

not specified (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.11

BayesDel_addAF

Benign

-0.53

BayesDel_noAF

Benign

-0.39

CADD

Uncertain

(source)

DANN

Benign

0.97

DEOGEN2

Benign

0.094

Eigen

Benign

-0.42

Eigen_PC

Benign

-0.16

FATHMM_MKL

Benign

0.59

LIST_S2

Benign

0.82

MetaRNN

Benign

0.0014

MetaSVM

Benign

-0.93

MutationAssessor

Benign

-0.14

PhyloP100

2.5

PrimateAI

Benign

0.40

PROVEAN

Benign

0.83

REVEL

Benign

0.21

Sift

Benign

0.77

Sift4G

Benign

0.55

Polyphen

0.077

Vest4

0.10

MPC

0.092

ClinPred

0.016

GERP RS

4.7

Varity_R

0.042

gMVP

0.30

Mutation Taster

=96/4

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over