15-36644592-C-T

Position:

• chr15-36644592-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Moderate BP6_Moderate BA1

The NM_001321759.2(CDIN1):​c.147+269C>T variant causes a intron change. The variant allele was found at a frequency of 0.954 in 152,210 control chromosomes in the GnomAD database, including 69,260 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.95 (69260 hom., cov: 30)
• Consequence: CDIN1 NM_001321759.2 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 3.98

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.4).
• BP6: Variant 15-36644592-C-T is Benign according to our data. Variant chr15-36644592-C-T is described in ClinVar as [Benign]. Clinvar id is 1294012.Status of the report is criteria_provided_single_submitter, 1 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.147+269C>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.147+269C>T		intron_variant		5	NM_001321759.2	ENSP00000455397.1

Frequencies

GnomAD3 genomes AF: 0.954 AC: 145100 AN: 152092 Hom.: 69221 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

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

GnomAD4 genome AF: 0.954 AC: 145196 AN: 152210 Hom.: 69260 Cov.: 30 AF XY: 0.956 AC XY: 71155 AN XY: 74420

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: 0.957 Hom.: 19317

Bravo AF: 0.951

Asia WGS AF: 0.949 AC: 3301 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	-0.40
CADD	Benign	18
DANN	Benign	0.77

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs4923721; hg19: chr15-36936793;