15-36580168-T-C

Position:

• chr15-36580168-T-C

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_001321759.2(CDIN1):​c.101+207T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.847 in 152,252 control chromosomes in the GnomAD database, including 54,789 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.85 (54789 hom., cov: 33)
• Consequence: CDIN1 NM_001321759.2 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.154

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]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BP6: Variant 15-36580168-T-C is Benign according to our data. Variant chr15-36580168-T-C is described in ClinVar as [Benign]. Clinvar id is 1244450.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.874 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CDIN1	NM_001321759.2	c.101+207T>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.101+207T>C		intron_variant		5	NM_001321759.2	ENSP00000455397.1

Frequencies

GnomAD3 genomes AF: 0.847 AC: 128836 AN: 152134 Hom.: 54742 Cov.: 33

Gnomad AFR AF: 0.795

Gnomad AMI AF: 0.725

Gnomad AMR AF: 0.887

Gnomad ASJ AF: 0.905

Gnomad EAS AF: 0.879

Gnomad SAS AF: 0.824

Gnomad FIN AF: 0.883

Gnomad MID AF: 0.962

Gnomad NFE AF: 0.861

Gnomad OTH AF: 0.859

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.847 AC: 128940 AN: 152252 Hom.: 54789 Cov.: 33 AF XY: 0.847 AC XY: 63047 AN XY: 74438

Gnomad4 AFR AF: 0.795

Gnomad4 AMR AF: 0.887

Gnomad4 ASJ AF: 0.905

Gnomad4 EAS AF: 0.879

Gnomad4 SAS AF: 0.824

Gnomad4 FIN AF: 0.883

Gnomad4 NFE AF: 0.861

Gnomad4 OTH AF: 0.860

Alfa AF: 0.849 Hom.: 6827

Bravo AF: 0.846

Asia WGS AF: 0.842 AC: 2928 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 18, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	14
DANN	Benign	0.72

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: rs6495842; hg19: chr15-36872369;