rs10492507

chr13-49250154-C-T

Variant summary

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

The NM_030911.4(CDADC1):c.177+1189C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.111 in 152,164 control chromosomes in the GnomAD database, including 1,268 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 0.11 (1268 hom., cov: 32)
• Consequence: CDADC1 NM_030911.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.235

Genes affected

CDADC1 (HGNC:20299): (cytidine and dCMP deaminase domain containing 1) Enables several functions, including cytidine deaminase activity; importin-alpha family protein binding activity; and protein homodimerization activity. Involved in DNA cytosine deamination and cytidine deamination. Located in cytoplasm and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.156 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CDADC1	NM_030911.4	c.177+1189C>T		intron_variant		ENST00000251108.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CDADC1	ENST00000251108.10	c.177+1189C>T		intron_variant		1	NM_030911.4	P1

Frequencies

GnomAD3 genomes AF: 0.111 AC: 16931 AN: 152046 Hom.: 1269 Cov.: 32

Gnomad AFR AF: 0.0297

Gnomad AMI AF: 0.414

Gnomad AMR AF: 0.0977

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.110

Gnomad FIN AF: 0.154

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.111 AC: 16931 AN: 152164 Hom.: 1268 Cov.: 32 AF XY: 0.110 AC XY: 8162 AN XY: 74378

Gnomad4 AFR AF: 0.0298

Gnomad4 AMR AF: 0.0974

Gnomad4 ASJ AF: 0.175

Gnomad4 EAS AF: 0.00154

Gnomad4 SAS AF: 0.110

Gnomad4 FIN AF: 0.154

Gnomad4 NFE AF: 0.159

Gnomad4 OTH AF: 0.110

Alfa AF: 0.139 Hom.: 446

Bravo AF: 0.105

Asia WGS AF: 0.0420 AC: 146 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	3.8
Dann	Benign	0.80

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: rs10492507; hg19: chr13-49824290;