15-36645204-G-T

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

2

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]

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
CDIN1NM_001321759.2 linkuse as main transcriptc.148-19G>T intron_variant ENST00000566621.6 NP_001308688.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CDIN1ENST00000566621.6 linkuse as main transcriptc.148-19G>T intron_variant 5 NM_001321759.2 ENSP00000455397 P1Q9Y2V0-1
ENST00000565366.1 linkuse as main transcriptn.122-3244C>A intron_variant, non_coding_transcript_variant 3

Frequencies

GnomAD3 genomes
AF:
0.954
AC:
145138
AN:
152124
Hom.:
69242
Cov.:
31
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.:
30
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.:
31
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 submitterclinical testingGeneDxAug 16, 2018- -
Benign, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpJan 31, 2024- -
Benign, criteria provided, single submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -
not specified Benign:1
Benign, criteria provided, single submitterclinical testingPreventionGenetics, part of Exact Sciences-- -
Congenital dyserythropoietic anemia type type 1B Benign:1
Benign, criteria provided, single submitterclinical testingGenome-Nilou LabJul 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.

Other links and lift over

dbSNP: rs11073191; hg19: chr15-36937405; API