Variant rs75993383 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.2174+20G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00473 in 1,613,924 control chromosomes in the GnomAD database, including 197 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.022 ( 105 hom., cov: 33)

Exomes 𝑓: 0.0030 ( 92 hom. )

Consequence

CDAN1
NM_138477.4 intron

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: -0.299

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:

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=-0.79).

BP6

Variant 15-42730578-C-T is Benign according to our data. Variant chr15-42730578-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 262369.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.069 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CDAN1	NM_138477.4 linkuse as main transcript	c.2174+20G>A		intron_variant		ENST00000356231.4	NP_612486.2

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	Appris	UniProt
CDAN1	ENST00000356231.4 linkuse as main transcript	c.2174+20G>A	intron_variant	1	NM_138477.4	ENSP00000348564	P1	Q8IWY9-2
CDAN1	ENST00000562465.5 linkuse as main transcript	c.167+20G>A	intron_variant, NMD_transcript_variant	1		ENSP00000454246
CDAN1	ENST00000643434.1 linkuse as main transcript	c.*1352+20G>A	intron_variant, NMD_transcript_variant			ENSP00000494699

Frequencies

GnomAD3 genomes

AF:

0.0214

AC:

3262

AN:

152208

Hom.:

102

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0706

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0121

Gnomad ASJ

AF:

0.00230

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.0316

Gnomad NFE

AF:

0.00123

Gnomad OTH

AF:

0.0230

GnomAD3 exomes

AF:

0.00638

AC:

1599

AN:

250794

Hom.:

AF XY:

0.00498

AC XY:

676

AN XY:

135770

show subpopulations

Gnomad AFR exome

AF:

0.0700

Gnomad AMR exome

AF:

0.00741

Gnomad ASJ exome

AF:

0.00328

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.0000327

Gnomad FIN exome

AF:

0.0000462

Gnomad NFE exome

AF:

0.00121

Gnomad OTH exome

AF:

0.00637

GnomAD4 exome

AF:

0.00297

AC:

4339

AN:

1461598

Hom.:

Cov.:

AF XY:

0.00267

AC XY:

1940

AN XY:

727108

show subpopulations

Gnomad4 AFR exome

AF:

0.0727

Gnomad4 AMR exome

AF:

0.00776

Gnomad4 ASJ exome

AF:

0.00253

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.000104

Gnomad4 FIN exome

AF:

0.0000936

Gnomad4 NFE exome

AF:

0.000833

Gnomad4 OTH exome

AF:

0.00795

GnomAD4 genome

AF:

0.0216

AC:

3292

AN:

152326

Hom.:

105

Cov.:

AF XY:

0.0206

AC XY:

1534

AN XY:

74490

show subpopulations

Gnomad4 AFR

AF:

0.0712

Gnomad4 AMR

AF:

0.0121

Gnomad4 ASJ

AF:

0.00230

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.00123

Gnomad4 OTH

AF:

0.0227

Alfa

AF:

0.0157

Hom.:

Bravo

AF:

0.0248

Asia WGS

AF:

0.00722

AC:

AN:

3478

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Likely benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 26, 2024	- -

not specified

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

Anemia, congenital dyserythropoietic, type 1a

Benign:1

Benign, criteria provided, single submitter

clinical testing

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

Nov 03, 2023

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

2.8

DANN

Benign

0.62

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