dbSNP rs7183415: CDIN1:p.Tyr141Tyr (chr15-36691761-T-C) – ACMG Classification: Benign (-21 pts)

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_001321759.2(CDIN1):c.423T>C(p.Tyr141Tyr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.107 in 1,587,854 control chromosomes in the GnomAD database, including 11,535 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.11 ( 1134 hom., cov: 30)

Exomes 𝑓: 0.11 ( 10401 hom. )

Consequence

CDIN1
NM_001321759.2 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: 2.42

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.54).

BP6

Variant 15-36691761-T-C is Benign according to our data. Variant chr15-36691761-T-C is described in ClinVar as [Benign]. Clinvar id is 257533.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=2.42 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.365 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CDIN1	NM_001321759.2 link	c.423T>C	p.Tyr141Tyr	synonymous_variant	Exon 6 of 11	ENST00000566621.6	NP_001308688.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CDIN1	ENST00000566621.6 link	c.423T>C	p.Tyr141Tyr	synonymous_variant	Exon 6 of 11	5	NM_001321759.2	ENSP00000455397.1		Q9Y2V0-1

Frequencies

GnomAD3 genomes

AF:

0.106

AC:

16156

AN:

151974

Hom.:

1133

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0993

Gnomad AMI

AF:

0.0921

Gnomad AMR

AF:

0.0874

Gnomad ASJ

AF:

0.0744

Gnomad EAS

AF:

0.378

Gnomad SAS

AF:

0.205

Gnomad FIN

AF:

0.0688

Gnomad MID

AF:

0.0601

Gnomad NFE

AF:

0.0957

Gnomad OTH

AF:

0.0881

GnomAD3 exomes

AF:

0.122

AC:

27222

AN:

223028

Hom.:

2395

AF XY:

0.124

AC XY:

14779

AN XY:

119548

show subpopulations

Gnomad AFR exome

AF:

0.108

Gnomad AMR exome

AF:

0.0778

Gnomad ASJ exome

AF:

0.0743

Gnomad EAS exome

AF:

0.377

Gnomad SAS exome

AF:

0.194

Gnomad FIN exome

AF:

0.0712

Gnomad NFE exome

AF:

0.0929

Gnomad OTH exome

AF:

0.102

GnomAD4 exome

AF:

0.107

AC:

153381

AN:

1435764

Hom.:

10401

Cov.:

AF XY:

0.109

AC XY:

77355

AN XY:

712904

show subpopulations

Gnomad4 AFR exome

AF:

0.108

Gnomad4 AMR exome

AF:

0.0783

Gnomad4 ASJ exome

AF:

0.0739

Gnomad4 EAS exome

AF:

0.367

Gnomad4 SAS exome

AF:

0.188

Gnomad4 FIN exome

AF:

0.0728

Gnomad4 NFE exome

AF:

0.0947

Gnomad4 OTH exome

AF:

0.114

GnomAD4 genome

AF:

0.106

AC:

16171

AN:

152090

Hom.:

1134

Cov.:

AF XY:

0.108

AC XY:

8040

AN XY:

74322

show subpopulations

Gnomad4 AFR

AF:

0.0995

Gnomad4 AMR

AF:

0.0874

Gnomad4 ASJ

AF:

0.0744

Gnomad4 EAS

AF:

0.379

Gnomad4 SAS

AF:

0.205

Gnomad4 FIN

AF:

0.0688

Gnomad4 NFE

AF:

0.0957

Gnomad4 OTH

AF:

0.0886

Alfa

AF:

0.0956

Hom.:

1376

Bravo

AF:

0.105

Asia WGS

AF:

0.248

AC:

862

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Jun 09, 2021

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not specified

Benign:1

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.54

CADD

Benign

9.7

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