Genetic Variant CDIN1:c.274-82T>A (chr15-36657751-T-A) – ACMG Classification: Benign (-18 pts)

Variant summary

Our verdict is Benign. The variant received -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBA1

The NM_001321759.2(CDIN1):c.274-82T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.96 in 1,068,884 control chromosomes in the GnomAD database, including 492,603 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.95 ( 69361 hom., cov: 31)

Exomes 𝑓: 0.96 ( 423242 hom. )

Consequence

CDIN1
NM_001321759.2 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 0.237

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 links:

ENSG00000261191 (HGNC:):

ENSG00000261191 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -18 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.44).

BP6

Variant 15-36657751-T-A is Benign according to our data. Variant chr15-36657751-T-A is described in ClinVar as [Benign]. Clinvar id is 1192629.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CDIN1	NM_001321759.2 link	c.274-82T>A		intron_variant	Intron 4 of 10	ENST00000566621.6	NP_001308688.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CDIN1	ENST00000566621.6 link	c.274-82T>A		intron_variant	Intron 4 of 10	5	NM_001321759.2	ENSP00000455397.1		Q9Y2V0-1

Frequencies

GnomAD3 genomes

AF:

0.955

AC:

145204

AN:

152092

Hom.:

69321

Cov.:

show subpopulations

Gnomad AFR

AF:

0.937

Gnomad AMI

AF:

0.942

Gnomad AMR

AF:

0.952

Gnomad ASJ

AF:

0.959

Gnomad EAS

AF:

0.999

Gnomad SAS

AF:

0.948

Gnomad FIN

AF:

0.989

Gnomad MID

AF:

0.953

Gnomad NFE

AF:

0.958

Gnomad OTH

AF:

0.954

GnomAD4 exome

AF:

0.961

AC:

880717

AN:

916674

Hom.:

423242

AF XY:

0.960

AC XY:

446817

AN XY:

465314

show subpopulations

African (AFR)

AF:

0.939

AC:

19842

AN:

21130

American (AMR)

AF:

0.968

AC:

28383

AN:

29332

Ashkenazi Jewish (ASJ)

AF:

0.960

AC:

20052

AN:

20892

East Asian (EAS)

AF:

0.999

AC:

32852

AN:

32878

South Asian (SAS)

AF:

0.953

AC:

59091

AN:

62010

European-Finnish (FIN)

AF:

0.986

AC:

47623

AN:

48278

Middle Eastern (MID)

AF:

0.960

AC:

4458

AN:

4646

European-Non Finnish (NFE)

AF:

0.959

AC:

628818

AN:

656036

Other (OTH)

AF:

0.955

AC:

39598

AN:

41472

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1618

3236

4855

6473

8091

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.955

AC:

145301

AN:

152210

Hom.:

69361

Cov.:

AF XY:

0.957

AC XY:

71208

AN XY:

74428

show subpopulations

African (AFR)

AF:

0.937

AC:

38912

AN:

41542

American (AMR)

AF:

0.953

AC:

14565

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.959

AC:

3328

AN:

3470

East Asian (EAS)

AF:

0.999

AC:

5173

AN:

5180

South Asian (SAS)

AF:

0.948

AC:

4570

AN:

4820

European-Finnish (FIN)

AF:

0.989

AC:

10498

AN:

10620

Middle Eastern (MID)

AF:

0.949

AC:

279

AN:

294

European-Non Finnish (NFE)

AF:

0.958

AC:

65108

AN:

67970

Other (OTH)

AF:

0.951

AC:

2009

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

351

702

1052

1403

1754

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.959

Hom.:

8158

Bravo

AF:

0.952

Asia WGS

AF:

0.949

AC:

3300

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Jun 18, 2021

GeneDx

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

- -

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

BayesDel_noAF

Benign

-0.44

CADD

Benign

(source)

DANN

Benign

0.80

PhyloP100

0.24

Mutation Taster

=100/0

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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15-36657751-T-A

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over