Variant chr15-36645204-G-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.148-19G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.959 in 1,543,190 control chromosomes in the GnomAD database, including 709,089 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.95 ( 69281 hom., cov: 31)

Exomes 𝑓: 0.96 ( 639808 hom. )

Consequence

CDIN1
NM_001321759.2 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:5

Conservation

PhyloP100: 1.11

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:

(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=-0.97).

BP6

Variant 15-36645204-G-T is Benign according to our data. Variant chr15-36645204-G-T is described in ClinVar as [Benign]. Clinvar id is 257531.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 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.148-19G>T		intron_variant		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.148-19G>T		intron_variant		5	NM_001321759.2	ENSP00000455397	P1	Q9Y2V0-1
	ENST00000565366.1 linkuse as main transcript	n.122-3244C>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes

AF:

0.954

AC:

145138

AN:

152124

Hom.:

69242

Cov.:

show subpopulations

Gnomad AFR

AF:

0.935

Gnomad AMI

AF:

0.942

Gnomad AMR

AF:

0.952

Gnomad ASJ

AF:

0.961

Gnomad EAS

AF:

0.999

Gnomad SAS

AF:

0.949

Gnomad FIN

AF:

0.988

Gnomad MID

AF:

0.953

Gnomad NFE

AF:

0.958

Gnomad OTH

AF:

0.954

GnomAD3 exomes

AF:

0.963

AC:

146807

AN:

152376

Hom.:

70754

AF XY:

0.963

AC XY:

77689

AN XY:

80692

show subpopulations

Gnomad AFR exome

AF:

0.934

Gnomad AMR exome

AF:

0.970

Gnomad ASJ exome

AF:

0.962

Gnomad EAS exome

AF:

0.999

Gnomad SAS exome

AF:

0.954

Gnomad FIN exome

AF:

0.987

Gnomad NFE exome

AF:

0.956

Gnomad OTH exome

AF:

0.954

GnomAD4 exome

AF:

0.959

AC:

1333924

AN:

1390948

Hom.:

639808

Cov.:

AF XY:

0.959

AC XY:

657928

AN XY:

686248

show subpopulations

Gnomad4 AFR exome

AF:

0.936

Gnomad4 AMR exome

AF:

0.968

Gnomad4 ASJ exome

AF:

0.962

Gnomad4 EAS exome

AF:

0.999

Gnomad4 SAS exome

AF:

0.953

Gnomad4 FIN exome

AF:

0.985

Gnomad4 NFE exome

AF:

0.957

Gnomad4 OTH exome

AF:

0.955

GnomAD4 genome

AF:

0.954

AC:

145234

AN:

152242

Hom.:

69281

Cov.:

AF XY:

0.956

AC XY:

71163

AN XY:

74422

show subpopulations

Gnomad4 AFR

AF:

0.935

Gnomad4 AMR

AF:

0.953

Gnomad4 ASJ

AF:

0.961

Gnomad4 EAS

AF:

0.999

Gnomad4 SAS

AF:

0.949

Gnomad4 FIN

AF:

0.988

Gnomad4 NFE

AF:

0.958

Gnomad4 OTH

AF:

0.951

Alfa

AF:

0.958

Hom.:

8050

Bravo

AF:

0.951

Asia WGS

AF:

0.949

AC:

3300

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Benign, criteria provided, single submitter	clinical testing	GeneDx	Aug 16, 2018	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 31, 2024	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

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

-0.97

CADD

Benign

0.16

DANN

Benign

0.27

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