Variant chr15-42724277-A-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_138477.4(CDAN1):c.*214T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.29 in 590,932 control chromosomes in the GnomAD database, including 35,840 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.39 ( 17635 hom., cov: 33)

Exomes 𝑓: 0.26 ( 18205 hom. )

Consequence

CDAN1
NM_138477.4 3_prime_UTR

Scores

Clinical Significance

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

Conservation

PhyloP100: 1.43

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=-0.88).

BP6

Variant 15-42724277-A-G is Benign according to our data. Variant chr15-42724277-A-G is described in ClinVar as [Benign]. Clinvar id is 315915.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.828 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.*214T>C		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.*214T>C		3_prime_UTR_variant	28/28	1	NM_138477.4	P1	Q8IWY9-2
	ENST00000615831.1 linkuse as main transcript	n.176A>G		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes

AF:

0.389

AC:

59180

AN:

152052

Hom.:

17574

Cov.:

show subpopulations

Gnomad AFR

AF:

0.835

Gnomad AMI

AF:

0.0923

Gnomad AMR

AF:

0.197

Gnomad ASJ

AF:

0.300

Gnomad EAS

AF:

0.250

Gnomad SAS

AF:

0.422

Gnomad FIN

AF:

0.237

Gnomad MID

AF:

0.269

Gnomad NFE

AF:

0.203

Gnomad OTH

AF:

0.339

GnomAD4 exome

AF:

0.255

AC:

111889

AN:

438762

Hom.:

18205

Cov.:

AF XY:

0.265

AC XY:

61495

AN XY:

231874

show subpopulations

Gnomad4 AFR exome

AF:

0.840

Gnomad4 AMR exome

AF:

0.145

Gnomad4 ASJ exome

AF:

0.294

Gnomad4 EAS exome

AF:

0.247

Gnomad4 SAS exome

AF:

0.434

Gnomad4 FIN exome

AF:

0.244

Gnomad4 NFE exome

AF:

0.202

Gnomad4 OTH exome

AF:

0.275

GnomAD4 genome

AF:

0.390

AC:

59295

AN:

152170

Hom.:

17635

Cov.:

AF XY:

0.386

AC XY:

28748

AN XY:

74408

show subpopulations

Gnomad4 AFR

AF:

0.836

Gnomad4 AMR

AF:

0.197

Gnomad4 ASJ

AF:

0.300

Gnomad4 EAS

AF:

0.251

Gnomad4 SAS

AF:

0.421

Gnomad4 FIN

AF:

0.237

Gnomad4 NFE

AF:

0.203

Gnomad4 OTH

AF:

0.335

Alfa

AF:

0.233

Hom.:

5348

Bravo

AF:

0.400

Asia WGS

AF:

0.355

AC:

1234

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

Congenital dyserythropoietic anemia, type I

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jan 12, 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

-0.88

CADD

Benign

8.2

DANN

Benign

0.51

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