NM_001321759.2:c.148-19G>T

Variant names:

• chr15-36645204-G-T
• rs11073191
• NM_001321759.2:c.148-19G>T

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

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
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:5
• Conservation: PhyloP100: 1.11
• Publications: 6 publications found

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 Gene-Disease associations (from GenCC):

• congenital dyserythropoietic anemia type type 1B

  Inheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
• congenital dyserythropoietic anemia type 1

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

ENSG00000261191 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 VariationId 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 rank	MANE	Protein	UniProt
CDIN1	NM_001321759.2	c.148-19G>T		intron_variant	Intron 2 of 10	ENST00000566621.6	NP_001308688.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CDIN1	ENST00000566621.6	c.148-19G>T		intron_variant	Intron 2 of 10	5	NM_001321759.2	ENSP00000455397.1

Frequencies

GnomAD3 genomes AF: 0.954 AC: 145138 AN: 152124 Hom.: 69242 Cov.: 31

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

GnomAD2 exomes AF: 0.963 AC: 146807 AN: 152376 AF XY: 0.963

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 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.: 30 AF XY: 0.959 AC XY: 657928 AN XY: 686248

African (AFR) AF: 0.936 AC: 29287 AN: 31290

American (AMR) AF: 0.968 AC: 34059 AN: 35178

Ashkenazi Jewish (ASJ) AF: 0.962 AC: 24093 AN: 25048

East Asian (EAS) AF: 0.999 AC: 35633 AN: 35666

South Asian (SAS) AF: 0.953 AC: 74353 AN: 78016

European-Finnish (FIN) AF: 0.985 AC: 48530 AN: 49258

Middle Eastern (MID) AF: 0.961 AC: 5399 AN: 5620

European-Non Finnish (NFE) AF: 0.957 AC: 1027469 AN: 1073168

Other (OTH) AF: 0.955 AC: 55101 AN: 57704

GnomAD4 genome AF: 0.954 AC: 145234 AN: 152242 Hom.: 69281 Cov.: 31 AF XY: 0.956 AC XY: 71163 AN XY: 74422

African (AFR) AF: 0.935 AC: 38817 AN: 41532

American (AMR) AF: 0.953 AC: 14568 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.961 AC: 3338 AN: 3472

East Asian (EAS) AF: 0.999 AC: 5169 AN: 5176

South Asian (SAS) AF: 0.949 AC: 4581 AN: 4826

European-Finnish (FIN) AF: 0.988 AC: 10470 AN: 10596

Middle Eastern (MID) AF: 0.949 AC: 279 AN: 294

European-Non Finnish (NFE) AF: 0.958 AC: 65142 AN: 68026

Other (OTH) AF: 0.951 AC: 2011 AN: 2114

Alfa AF: 0.958 Hom.: 18093

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

Submissions by phenotype

not provided Benign:3

Aug 16, 2018

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

- -

Congenital dyserythropoietic anemia type type 1B Benign:1

Jul 14, 2021

Genome-Nilou Lab

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	-0.97
CADD	Benign	0.16
DANN	Benign	0.27
PhyloP100		1.1
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs11073191; hg19: chr15-36937405;