15-36654102-C-G

Variant names:

Variant summary

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

The NM_001321759.2(CDIN1):c.217C>G(p.Leu73Val) variant causes a missense change. The variant allele was found at a frequency of 0.472 in 1,573,246 control chromosomes in the GnomAD database, including 177,965 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.44 ( 15284 hom., cov: 31)

Exomes 𝑓: 0.47 ( 162681 hom. )

Consequence

CDIN1
NM_001321759.2 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:5

Conservation

PhyloP100: 3.70

Publications

36 publications found

Variant links:

Genes affected

CDIN1 (HGNC:26929): (CDAN1 interacting nuclease 1) This gene encodes a protein with two predicted helix-turn-helix domains. Mutations in this gene were found in families with congenital dyserythropoietic anemia type Ib. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Mar 2014]

CDIN1 Gene-Disease associations (from GenCC):

congenital dyserythropoietic anemia type type 1B
Inheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
congenital dyserythropoietic anemia type 1
Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

CDIN1 links:

ENSG00000261191 (HGNC:):

ENSG00000261191 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=2.810986E-5).

BP6

Variant 15-36654102-C-G is Benign according to our data. Variant chr15-36654102-C-G is described in ClinVar as Benign. ClinVar VariationId is 257532.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.634 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CDIN1	NM_001321759.2 link	c.217C>G	p.Leu73Val	missense_variant	Exon 4 of 11	ENST00000566621.6	NP_001308688.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CDIN1	ENST00000566621.6 link	c.217C>G	p.Leu73Val	missense_variant	Exon 4 of 11	5	NM_001321759.2	ENSP00000455397.1		Q9Y2V0-1

Frequencies

GnomAD3 genomes

AF:

0.444

AC:

67364

AN:

151788

Hom.:

15280

Cov.:

show subpopulations

Gnomad AFR

AF:

0.395

Gnomad AMI

AF:

0.562

Gnomad AMR

AF:

0.360

Gnomad ASJ

AF:

0.440

Gnomad EAS

AF:

0.653

Gnomad SAS

AF:

0.595

Gnomad FIN

AF:

0.428

Gnomad MID

AF:

0.402

Gnomad NFE

AF:

0.467

Gnomad OTH

AF:

0.434

GnomAD2 exomes

AF:

0.462

AC:

89872

AN:

194482

AF XY:

0.473

show subpopulations

Gnomad AFR exome

AF:

0.380

Gnomad AMR exome

AF:

0.347

Gnomad ASJ exome

AF:

0.441

Gnomad EAS exome

AF:

0.651

Gnomad FIN exome

AF:

0.423

Gnomad NFE exome

AF:

0.455

Gnomad OTH exome

AF:

0.444

GnomAD4 exome

AF:

0.475

AC:

674933

AN:

1421340

Hom.:

162681

Cov.:

AF XY:

0.479

AC XY:

336490

AN XY:

703086

show subpopulations

African (AFR)

AF:

0.393

AC:

12947

AN:

32946

American (AMR)

AF:

0.350

AC:

13775

AN:

39352

Ashkenazi Jewish (ASJ)

AF:

0.440

AC:

11248

AN:

25542

East Asian (EAS)

AF:

0.674

AC:

25886

AN:

38392

South Asian (SAS)

AF:

0.589

AC:

47774

AN:

81062

European-Finnish (FIN)

AF:

0.436

AC:

22263

AN:

51072

Middle Eastern (MID)

AF:

0.479

AC:

2739

AN:

5716

European-Non Finnish (NFE)

AF:

0.469

AC:

510675

AN:

1088328

Other (OTH)

AF:

0.469

AC:

27626

AN:

58930

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.460

Heterozygous variant carriers

15576

31152

46728

62304

77880

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

15390

30780

46170

61560

76950

<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:

0.444

AC:

67397

AN:

151906

Hom.:

15284

Cov.:

AF XY:

0.445

AC XY:

33067

AN XY:

74250

show subpopulations

African (AFR)

AF:

0.395

AC:

16340

AN:

41398

American (AMR)

AF:

0.360

AC:

5492

AN:

15264

Ashkenazi Jewish (ASJ)

AF:

0.440

AC:

1528

AN:

3472

East Asian (EAS)

AF:

0.653

AC:

3363

AN:

5154

South Asian (SAS)

AF:

0.596

AC:

2875

AN:

4824

European-Finnish (FIN)

AF:

0.428

AC:

4511

AN:

10546

Middle Eastern (MID)

AF:

0.391

AC:

115

AN:

294

European-Non Finnish (NFE)

AF:

0.467

AC:

31745

AN:

67934

Other (OTH)

AF:

0.435

AC:

917

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1924

3847

5771

7694

9618

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

652

1304

1956

2608

3260

<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:

0.457

Hom.:

11605

Bravo

AF:

0.434

TwinsUK

AF:

0.459

AC:

1703

ALSPAC

AF:

0.476

AC:

1834

ESP6500AA

AF:

0.396

AC:

1239

ESP6500EA

AF:

0.459

AC:

3286

ExAC

AF:

0.413

AC:

48449

Asia WGS

AF:

0.572

AC:

1987

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Jun 09, 2021

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

This variant is associated with the following publications: (PMID: 29031773) -

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

not specified

Benign:1

PreventionGenetics, part of Exact Sciences

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Congenital dyserythropoietic anemia type type 1B

Benign:1

Jul 14, 2021

Genome-Nilou Lab

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.076

BayesDel_addAF

Benign

-0.50

BayesDel_noAF

Benign

-0.34

CADD

Uncertain

(source)

DANN

Uncertain

1.0

DEOGEN2

Benign

0.012

T;.;.;.;T;.;T

Eigen

Uncertain

0.47

Eigen_PC

Uncertain

0.53

FATHMM_MKL

Pathogenic

0.98

LIST_S2

Benign

0.82

.;T;T;T;.;T;T

MetaRNN

Benign

0.000028

T;T;T;T;T;T;T

MetaSVM

Benign

-0.91

MutationAssessor

Uncertain

2.2

M;.;.;.;M;.;M

PhyloP100

3.7

PROVEAN

Benign

-1.2

N;.;N;N;.;.;N

REVEL

Benign

0.15

Sift

Benign

0.079

T;.;D;T;.;.;T

Sift4G

Benign

0.098

T;.;D;T;.;.;T

Polyphen

0.88

P;.;.;.;P;.;P

Vest4

0.20

MPC

0.41

ClinPred

0.0098

GERP RS

5.5

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Varity_R

0.18

gMVP

0.36

Mutation Taster

=200/100

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over