Variant chr15-42724349-T-C 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_138477.4(CDAN1):c.*142A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.28 in 1,134,980 control chromosomes in the GnomAD database, including 58,741 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.41 ( 18329 hom., cov: 33)

Exomes 𝑓: 0.26 ( 40412 hom. )

Consequence

CDAN1
NM_138477.4 3_prime_UTR

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.950

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 links:

(HGNC:):

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 (BayesDel_noAF=-0.9).

BP6

Variant 15-42724349-T-C is Benign according to our data. Variant chr15-42724349-T-C is described in ClinVar as [Benign]. Clinvar id is 315916.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.833 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CDAN1	NM_138477.4 linkuse as main transcript	c.*142A>G		3_prime_UTR_variant	28/28	ENST00000356231.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CDAN1	ENST00000356231.4 linkuse as main transcript	c.*142A>G		3_prime_UTR_variant	28/28	1	NM_138477.4	P1	Q8IWY9-2
	ENST00000615831.1 linkuse as main transcript	n.248T>C		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes

AF:

0.405

AC:

61617

AN:

152104

Hom.:

18269

Cov.:

show subpopulations

Gnomad AFR

AF:

0.840

Gnomad AMI

AF:

0.0932

Gnomad AMR

AF:

0.220

Gnomad ASJ

AF:

0.320

Gnomad EAS

AF:

0.249

Gnomad SAS

AF:

0.427

Gnomad FIN

AF:

0.254

Gnomad MID

AF:

0.285

Gnomad NFE

AF:

0.227

Gnomad OTH

AF:

0.356

GnomAD4 exome

AF:

0.261

AC:

256406

AN:

982758

Hom.:

40412

Cov.:

AF XY:

0.267

AC XY:

132123

AN XY:

495586

show subpopulations

Gnomad4 AFR exome

AF:

0.860

Gnomad4 AMR exome

AF:

0.161

Gnomad4 ASJ exome

AF:

0.318

Gnomad4 EAS exome

AF:

0.246

Gnomad4 SAS exome

AF:

0.439

Gnomad4 FIN exome

AF:

0.254

Gnomad4 NFE exome

AF:

0.225

Gnomad4 OTH exome

AF:

0.296

GnomAD4 genome

AF:

0.406

AC:

61731

AN:

152222

Hom.:

18329

Cov.:

AF XY:

0.402

AC XY:

29910

AN XY:

74426

show subpopulations

Gnomad4 AFR

AF:

0.840

Gnomad4 AMR

AF:

0.220

Gnomad4 ASJ

AF:

0.320

Gnomad4 EAS

AF:

0.250

Gnomad4 SAS

AF:

0.427

Gnomad4 FIN

AF:

0.254

Gnomad4 NFE

AF:

0.227

Gnomad4 OTH

AF:

0.351

Alfa

AF:

0.239

Hom.:

5151

Bravo

AF:

0.418

Asia WGS

AF:

0.360

AC:

1251

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

Benign, criteria provided, single submitter	clinical testing	GeneDx	May 10, 2021	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Congenital dyserythropoietic anemia, type I

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jan 13, 2018

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

6.0

DANN

Benign

0.33

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