Variant 15-36654102-C-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -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

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:

CDIN1 (HGNC:):

CDIN1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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 id 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/exons	MANE	Protein	UniProt
CDIN1	NM_001321759.2 linkuse as main transcript	c.217C>G	p.Leu73Val	missense_variant	4/11	ENST00000566621.6	NP_001308688.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CDIN1	ENST00000566621.6 linkuse as main transcript	c.217C>G	p.Leu73Val	missense_variant	4/11	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

GnomAD3 exomes

AF:

0.462

AC:

89872

AN:

194482

Hom.:

21553

AF XY:

0.473

AC XY:

49075

AN XY:

103648

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 SAS exome

AF:

0.587

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

Gnomad4 AFR exome

AF:

0.393

Gnomad4 AMR exome

AF:

0.350

Gnomad4 ASJ exome

AF:

0.440

Gnomad4 EAS exome

AF:

0.674

Gnomad4 SAS exome

AF:

0.589

Gnomad4 FIN exome

AF:

0.436

Gnomad4 NFE exome

AF:

0.469

Gnomad4 OTH exome

AF:

0.469

GnomAD4 genome

AF:

0.444

AC:

67397

AN:

151906

Hom.:

15284

Cov.:

AF XY:

0.445

AC XY:

33067

AN XY:

74250

show subpopulations

Gnomad4 AFR

AF:

0.395

Gnomad4 AMR

AF:

0.360

Gnomad4 ASJ

AF:

0.440

Gnomad4 EAS

AF:

0.653

Gnomad4 SAS

AF:

0.596

Gnomad4 FIN

AF:

0.428

Gnomad4 NFE

AF:

0.467

Gnomad4 OTH

AF:

0.435

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

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 31, 2024	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 09, 2021	This variant is associated with the following publications: (PMID: 29031773) -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

Congenital dyserythropoietic anemia type type 1B

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 14, 2021

- -

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

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

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

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over