15-36645405-A-C

Position:

• chr15-36645405-A-C

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_001321759.2(CDIN1):​c.212+118A>C 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 894,820 control chromosomes in the GnomAD database, including 411,779 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.95 (69253 hom., cov: 30)
  • Exomes 𝑓: 0.96 (342526 hom.)
• Consequence: CDIN1 NM_001321759.2 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -2.09

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]

ENSG00000261191 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BP6: Variant 15-36645405-A-C is Benign according to our data. Variant chr15-36645405-A-C is described in ClinVar as [Benign]. Clinvar id is 1222423.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.212+118A>C		intron_variant		ENST00000566621.6	NP_001308688.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CDIN1	ENST00000566621.6	c.212+118A>C		intron_variant		5	NM_001321759.2	ENSP00000455397.1

Frequencies

GnomAD3 genomes AF: 0.954 AC: 145066 AN: 152038 Hom.: 69213 Cov.: 30

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

GnomAD4 exome AF: 0.960 AC: 713107 AN: 742664 Hom.: 342526 AF XY: 0.960 AC XY: 362979 AN XY: 378146

Gnomad4 AFR exome AF: 0.935

Gnomad4 AMR exome AF: 0.964

Gnomad4 ASJ exome AF: 0.962

Gnomad4 EAS exome AF: 0.999

Gnomad4 SAS exome AF: 0.954

Gnomad4 FIN exome AF: 0.985

Gnomad4 NFE exome AF: 0.957

Gnomad4 OTH exome AF: 0.954

GnomAD4 genome AF: 0.954 AC: 145163 AN: 152156 Hom.: 69253 Cov.: 30 AF XY: 0.956 AC XY: 71133 AN XY: 74382

Gnomad4 AFR AF: 0.935

Gnomad4 AMR AF: 0.952

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: 0.959 Hom.: 8147

Bravo AF: 0.951

Asia WGS AF: 0.950 AC: 3299 AN: 3474

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 18, 2021	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.53
DANN	Benign	0.66

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

Other links and lift over

dbSNP: rs11073192; hg19: chr15-36937606; COSMIC: COSV57712251;