15-42724025-TAAG-T

Position:

• chr15-42724025-TAAG-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_138477.4(CDAN1):​c.*463_*465del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0411 in 245,478 control chromosomes in the GnomAD database, including 660 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.056 (593 hom., cov: 32)
  • Exomes 𝑓: 0.017 (67 hom.)
• Consequence: CDAN1 NM_138477.4 3_prime_UTR
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.67

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]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 15-42724025-TAAG-T is Benign according to our data. Variant chr15-42724025-TAAG-T is described in ClinVar as [Likely_benign]. Clinvar id is 315911.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.17 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CDAN1	NM_138477.4	c.*463_*465del		3_prime_UTR_variant	28/28	ENST00000356231.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CDAN1	ENST00000356231.4	c.*463_*465del		3_prime_UTR_variant	28/28	1	NM_138477.4	P1
CDAN1	ENST00000562465.5	c.*1049_*1051del		3_prime_UTR_variant, NMD_transcript_variant	15/15	1
CDAN1	ENST00000563604.1	n.1610_1612del		non_coding_transcript_exon_variant	1/1
CDAN1	ENST00000643434.1	c.*3214_*3216del		3_prime_UTR_variant, NMD_transcript_variant	25/25

Frequencies

GnomAD3 genomes AF: 0.0559 AC: 8500 AN: 152120 Hom.: 591 Cov.: 32

Gnomad AFR AF: 0.174

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0215

Gnomad ASJ AF: 0.0297

Gnomad EAS AF: 0.0581

Gnomad SAS AF: 0.0280

Gnomad FIN AF: 0.000565

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.00510

Gnomad OTH AF: 0.0402

GnomAD4 exome AF: 0.0167 AC: 1559 AN: 93240 Hom.: 67 AF XY: 0.0178 AC XY: 873 AN XY: 49064

Gnomad4 AFR exome AF: 0.165

Gnomad4 AMR exome AF: 0.0105

Gnomad4 ASJ exome AF: 0.0306

Gnomad4 EAS exome AF: 0.0664

Gnomad4 SAS exome AF: 0.0287

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00406

Gnomad4 OTH exome AF: 0.0159

GnomAD4 genome AF: 0.0560 AC: 8519 AN: 152238 Hom.: 593 Cov.: 32 AF XY: 0.0541 AC XY: 4027 AN XY: 74458

Gnomad4 AFR AF: 0.174

Gnomad4 AMR AF: 0.0215

Gnomad4 ASJ AF: 0.0297

Gnomad4 EAS AF: 0.0583

Gnomad4 SAS AF: 0.0280

Gnomad4 FIN AF: 0.000565

Gnomad4 NFE AF: 0.00509

Gnomad4 OTH AF: 0.0402

Alfa AF: 0.0333 Hom.: 46

Bravo AF: 0.0626

Asia WGS AF: 0.0470 AC: 164 AN: 3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Congenital dyserythropoietic anemia Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.090		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

Other links and lift over

dbSNP: rs111961345; hg19: chr15-43016223;