15-36645204-G-T
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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
NM_001321759.2 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.11
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]
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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=-0.97).
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 | 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 | c.148-19G>T | intron_variant | 5 | NM_001321759.2 | ENSP00000455397 | P1 | |||
ENST00000565366.1 | n.122-3244C>A | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.954 AC: 145138AN: 152124Hom.: 69242 Cov.: 31
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GnomAD3 exomes AF: 0.963 AC: 146807AN: 152376Hom.: 70754 AF XY: 0.963 AC XY: 77689AN XY: 80692
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GnomAD4 exome AF: 0.959 AC: 1333924AN: 1390948Hom.: 639808 Cov.: 30 AF XY: 0.959 AC XY: 657928AN XY: 686248
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GnomAD4 genome AF: 0.954 AC: 145234AN: 152242Hom.: 69281 Cov.: 31 AF XY: 0.956 AC XY: 71163AN XY: 74422
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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
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at