rs10492506

Variant names:

• chr13-49250500-T-A
• rs10492506
• NM_030911.4:c.177+1535T>A

Your query was ambiguous. Multiple possible variants found:

• chr13-49250500-T-A
• chr13-49250500-T-C
• chr13-49250500-T-G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_030911.4(CDADC1):​c.177+1535T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: CDADC1 NM_030911.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.166
• Publications: 0 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).

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+1535T>A		intron	N/A	NP_112173.1	Q9BWV3-1
	CDADC1	NM_001193478.2		c.177+1535T>A		intron	N/A	NP_001180407.1
	CDADC1	NR_036439.2		n.290+1535T>A		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+1535T>A		intron	N/A	ENSP00000251108.6	Q9BWV3-1
	CDADC1	ENST00000466868.1	TSL:1	n.268+1535T>A		intron	N/A
	CDADC1	ENST00000496061.5	TSL:1	n.177+1535T>A		intron	N/A	ENSP00000434135.1	F2Z2J8

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	6.2
DANN	Benign	0.86
PhyloP100		0.17

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: rs10492506; hg19: chr13-49824636;