rs10518893

chr15-36605626-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001321759.2(CDIN1):c.101+25665A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0397 in 152,310 control chromosomes in the GnomAD database, including 178 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 0.040 (178 hom., cov: 32)
• Consequence: CDIN1 NM_001321759.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.119

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.48).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.132 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CDIN1	NM_001321759.2	c.101+25665A>G		intron_variant		ENST00000566621.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CDIN1	ENST00000566621.6	c.101+25665A>G		intron_variant		5	NM_001321759.2	P1

Frequencies

GnomAD3 genomes AF: 0.0397 AC: 6040 AN: 152192 Hom.: 180 Cov.: 32

Gnomad AFR AF: 0.0276

Gnomad AMI AF: 0.0330

Gnomad AMR AF: 0.0253

Gnomad ASJ AF: 0.0109

Gnomad EAS AF: 0.0237

Gnomad SAS AF: 0.141

Gnomad FIN AF: 0.0379

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0464

Gnomad OTH AF: 0.0335

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

GnomAD4 genome AF: 0.0397 AC: 6042 AN: 152310 Hom.: 178 Cov.: 32 AF XY: 0.0406 AC XY: 3024 AN XY: 74468

Gnomad4 AFR AF: 0.0276

Gnomad4 AMR AF: 0.0252

Gnomad4 ASJ AF: 0.0109

Gnomad4 EAS AF: 0.0237

Gnomad4 SAS AF: 0.141

Gnomad4 FIN AF: 0.0379

Gnomad4 NFE AF: 0.0464

Gnomad4 OTH AF: 0.0341

Alfa AF: 0.0399 Hom.: 50

Bravo AF: 0.0352

Asia WGS AF: 0.0930 AC: 323 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.48
Cadd	Benign	11
Dann	Benign	0.76

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: rs10518893; hg19: chr15-36897827;