rs10492507

Variant names:

• chr13-49250154-C-T
• rs10492507
• NM_030911.4:c.177+1189C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_030911.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CDADC1	NM_030911.4	MANE Select	c.177+1189C>T		intron	N/A	NP_112173.1	Q9BWV3-1
	CDADC1	NM_001193478.2		c.177+1189C>T		intron	N/A	NP_001180407.1
	CDADC1	NR_036439.2		n.290+1189C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CDADC1	ENST00000251108.10	TSL:1 MANE Select	c.177+1189C>T		intron	N/A	ENSP00000251108.6	Q9BWV3-1
	CDADC1	ENST00000466868.1	TSL:1	n.268+1189C>T		intron	N/A
	CDADC1	ENST00000496061.5	TSL:1	n.177+1189C>T		intron	N/A	ENSP00000434135.1	F2Z2J8

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

African (AFR) AF: 0.0298 AC: 1239 AN: 41538

American (AMR) AF: 0.0974 AC: 1489 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.175 AC: 608 AN: 3470

East Asian (EAS) AF: 0.00154 AC: 8 AN: 5182

South Asian (SAS) AF: 0.110 AC: 529 AN: 4814

European-Finnish (FIN) AF: 0.154 AC: 1624 AN: 10568

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.159 AC: 10785 AN: 67990

Other (OTH) AF: 0.110 AC: 231 AN: 2108

Alfa AF: 0.138 Hom.: 551

Bravo AF: 0.105

Asia WGS AF: 0.0420 AC: 146 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.8
DANN	Benign	0.80
PhyloP100		0.23
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: rs10492507; hg19: chr13-49824290;