rs12148445

Positions:

• chr15-36624457-T-G

Variant summary

Our verdict is Benign. Variant got -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

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 -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CDIN1	NM_001321759.2	c.102-19821T>G		intron_variant		ENST00000566621.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CDIN1	ENST00000566621.6	c.102-19821T>G		intron_variant		5	NM_001321759.2	P1

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

Gnomad4 AFR AF: 0.114

Gnomad4 AMR AF: 0.118

Gnomad4 ASJ AF: 0.134

Gnomad4 EAS AF: 0.0494

Gnomad4 SAS AF: 0.119

Gnomad4 FIN AF: 0.135

Gnomad4 NFE AF: 0.122

Gnomad4 OTH AF: 0.132

Alfa AF: 0.124 Hom.: 190

Bravo AF: 0.113

Asia WGS AF: 0.0780 AC: 271 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.24
CADD	Benign	18
DANN	Benign	0.82

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: rs12148445; hg19: chr15-36916658;