Variant chr15-36579756-C-T 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.-105C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.475 in 877,082 control chromosomes in the GnomAD database, including 100,152 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.48 ( 17784 hom., cov: 33)

Exomes 𝑓: 0.47 ( 82368 hom. )

Consequence

CDIN1
NM_001321759.2 5_prime_UTR

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.0400

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.77).

BP6

Variant 15-36579756-C-T is Benign according to our data. Variant chr15-36579756-C-T is described in ClinVar as [Benign]. Clinvar id is 1181468.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.543 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.-105C>T		5_prime_UTR_variant	1/11	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.-105C>T		5_prime_UTR_variant	1/11	5	NM_001321759.2	ENSP00000455397	P1	Q9Y2V0-1

Frequencies

GnomAD3 genomes

AF:

0.481

AC:

73003

AN:

151928

Hom.:

17765

Cov.:

show subpopulations

Gnomad AFR

AF:

0.466

Gnomad AMI

AF:

0.366

Gnomad AMR

AF:

0.553

Gnomad ASJ

AF:

0.477

Gnomad EAS

AF:

0.477

Gnomad SAS

AF:

0.468

Gnomad FIN

AF:

0.485

Gnomad MID

AF:

0.513

Gnomad NFE

AF:

0.475

Gnomad OTH

AF:

0.487

GnomAD4 exome

AF:

0.474

AC:

343951

AN:

725036

Hom.:

82368

Cov.:

AF XY:

0.473

AC XY:

175668

AN XY:

371100

show subpopulations

Gnomad4 AFR exome

AF:

0.464

Gnomad4 AMR exome

AF:

0.605

Gnomad4 ASJ exome

AF:

0.457

Gnomad4 EAS exome

AF:

0.442

Gnomad4 SAS exome

AF:

0.465

Gnomad4 FIN exome

AF:

0.484

Gnomad4 NFE exome

AF:

0.471

Gnomad4 OTH exome

AF:

0.475

GnomAD4 genome

AF:

0.481

AC:

73067

AN:

152046

Hom.:

17784

Cov.:

AF XY:

0.481

AC XY:

35752

AN XY:

74344

show subpopulations

Gnomad4 AFR

AF:

0.466

Gnomad4 AMR

AF:

0.553

Gnomad4 ASJ

AF:

0.477

Gnomad4 EAS

AF:

0.476

Gnomad4 SAS

AF:

0.469

Gnomad4 FIN

AF:

0.485

Gnomad4 NFE

AF:

0.475

Gnomad4 OTH

AF:

0.489

Alfa

AF:

0.479

Hom.:

14530

Bravo

AF:

0.488

Asia WGS

AF:

0.464

AC:

1617

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	Jun 18, 2021	- -

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

BayesDel_noAF

Benign

-0.77

CADD

Benign

DANN

Benign

0.73

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

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