chr15-36624457-T-G

Variant names:

• chr15-36624457-T-G
• rs12148445
• NM_001321759.2:c.102-19821T>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_001321759.2(CDIN1):​c.102-19821T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.118 in 152,256 control chromosomes in the GnomAD database, including 1,057 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.12 (1057 hom., cov: 32)
• Consequence: CDIN1 NM_001321759.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.94
• Publications: 1 publications found

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]

CDIN1 Gene-Disease associations (from GenCC):

• congenital dyserythropoietic anemia type type 1B

  Inheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
• congenital dyserythropoietic anemia type 1

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.24).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.12 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001321759.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CDIN1	NM_001321759.2	MANE Select	c.102-19821T>G		intron	N/A	NP_001308688.1
	CDIN1	NM_001321761.2		c.102-19821T>G		intron	N/A	NP_001308690.1
	CDIN1	NM_001290233.2		c.102-19821T>G		intron	N/A	NP_001277162.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CDIN1	ENST00000566621.6	TSL:5 MANE Select	c.102-19821T>G		intron	N/A	ENSP00000455397.1
	CDIN1	ENST00000437989.6	TSL:1	c.102-19821T>G		intron	N/A	ENSP00000401362.2
	CDIN1	ENST00000562877.5	TSL:1	c.-193-19821T>G		intron	N/A	ENSP00000457854.1

Frequencies

GnomAD3 genomes AF: 0.118 AC: 18006 AN: 152138 Hom.: 1056 Cov.: 32

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.123

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.0491

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.172

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.132

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

GnomAD4 genome AF: 0.118 AC: 18012 AN: 152256 Hom.: 1057 Cov.: 32 AF XY: 0.119 AC XY: 8893 AN XY: 74456

African (AFR) AF: 0.114 AC: 4750 AN: 41548

American (AMR) AF: 0.118 AC: 1805 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.134 AC: 464 AN: 3472

East Asian (EAS) AF: 0.0494 AC: 256 AN: 5186

South Asian (SAS) AF: 0.119 AC: 573 AN: 4824

European-Finnish (FIN) AF: 0.135 AC: 1436 AN: 10600

Middle Eastern (MID) AF: 0.168 AC: 49 AN: 292

European-Non Finnish (NFE) AF: 0.122 AC: 8289 AN: 68018

Other (OTH) AF: 0.132 AC: 278 AN: 2110

Alfa AF: 0.120 Hom.: 1600

Bravo AF: 0.113

Asia WGS AF: 0.0780 AC: 271 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.24
CADD	Benign	18
DANN	Benign	0.82
PhyloP100		1.9
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs12148445; hg19: chr15-36916658;