Genetic Variant CDIN1:c.147+269C>T (chr15-36644592-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_ModerateBP6_ModerateBA1

The NM_001321759.2(CDIN1):c.147+269C>T variant causes a intron change. The variant allele was found at a frequency of 0.954 in 152,210 control chromosomes in the GnomAD database, including 69,260 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.95 ( 69260 hom., cov: 30)

Consequence

CDIN1
NM_001321759.2 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 3.98

Publications

0 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:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.4).

BP6

Variant 15-36644592-C-T is Benign according to our data. Variant chr15-36644592-C-T is described in ClinVar as Benign. ClinVar VariationId is 1294012.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001321759.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
CDIN1	NM_001321759.2	MANE Select	c.147+269C>T	intron	N/A	NP_001308688.1	Q9Y2V0-1
CDIN1	NM_001321761.2		c.147+269C>T	intron	N/A	NP_001308690.1	H3BS01
CDIN1	NM_001290233.2		c.147+269C>T	intron	N/A	NP_001277162.1	A0A2R8YD89

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
CDIN1	ENST00000566621.6	TSL:5 MANE Select	c.147+269C>T	intron	N/A	ENSP00000455397.1	Q9Y2V0-1
CDIN1	ENST00000437989.6	TSL:1	c.147+269C>T	intron	N/A	ENSP00000401362.2	Q9Y2V0-1
CDIN1	ENST00000562877.5	TSL:1	c.-148+269C>T	intron	N/A	ENSP00000457854.1	Q9Y2V0-2

Frequencies

GnomAD3 genomes

AF:

0.954

AC:

145100

AN:

152092

Hom.:

69221

Cov.:

show subpopulations

Gnomad AFR

AF:

0.935

Gnomad AMI

AF:

0.942

Gnomad AMR

AF:

0.952

Gnomad ASJ

AF:

0.961

Gnomad EAS

AF:

0.999

Gnomad SAS

AF:

0.949

Gnomad FIN

AF:

0.988

Gnomad MID

AF:

0.953

Gnomad NFE

AF:

0.958

Gnomad OTH

AF:

0.954

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.954

AC:

145196

AN:

152210

Hom.:

69260

Cov.:

AF XY:

0.956

AC XY:

71155

AN XY:

74420

show subpopulations

African (AFR)

AF:

0.935

AC:

38785

AN:

41498

American (AMR)

AF:

0.953

AC:

14564

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.961

AC:

3338

AN:

3472

East Asian (EAS)

AF:

0.999

AC:

5153

AN:

5160

South Asian (SAS)

AF:

0.949

AC:

4577

AN:

4824

European-Finnish (FIN)

AF:

0.988

AC:

10487

AN:

10616

Middle Eastern (MID)

AF:

0.949

AC:

279

AN:

294

European-Non Finnish (NFE)

AF:

0.958

AC:

65141

AN:

68028

Other (OTH)

AF:

0.951

AC:

2013

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.509

Heterozygous variant carriers

351

702

1053

1404

1755

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

912

1824

2736

3648

4560

<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:

0.957

Hom.:

24984

Bravo

AF:

0.951

Asia WGS

AF:

0.949

AC:

3301

AN:

3478

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.40

CADD

Benign

(source)

DANN

Benign

0.77

PhyloP100

4.0

Mutation Taster

=97/3

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over