1-93264857-AGG-CGA

Variant names:

• chr1-93264857-AGG-CGA
• NM_001378204.1:c.3841_3843delAGGinsCGA
• CCDC18 p.1282

Variant summary

Our verdict is Likely benign. The variant received -1 ACMG points: 0P and 1B. BP7

The NM_001378204.1(CCDC18):​c.3841_3843delAGGinsCGA​(p.1282) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type MNV, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. R1281R) has been classified as Benign.

• Frequency: Genomes: not found (cov: 32)
• Consequence: CCDC18 NM_001378204.1 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.08
• Publications: 0 publications found

Genes affected

CCDC18 (HGNC:30370): (coiled-coil domain containing 18)

CCDC18-AS1 (HGNC:52262): (CCDC18 antisense RNA 1)

ACMG classification

Our verdict: Likely_benign. The variant received -1 ACMG points.

• BP7: Synonymous conserved (PhyloP=3.08 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001378204.1. 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
	CCDC18	NM_001378204.1	MANE Select	c.3841_3843delAGGinsCGA	p.1282	synonymous	N/A	NP_001365133.1	A0A8I5KWA2
	CCDC18	NM_001306076.1		c.3838_3840delAGGinsCGA	p.1281	synonymous	N/A	NP_001293005.1	Q6PH87
	CCDC18	NM_206886.4		c.3841_3843delAGGinsCGA	p.1282	synonymous	N/A	NP_996769.3	Q6PH87

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC18	ENST00000690025.1	MANE Select	c.3841_3843delAGGinsCGA	p.1282	synonymous	N/A	ENSP00000510597.1	A0A8I5KWA2
	CCDC18	ENST00000401026.7	TSL:1	c.3841_3843delAGGinsCGA	p.1282	synonymous	N/A	ENSP00000383808.3	E9PFB9
	CCDC18	ENST00000447456.1	TSL:1	n.597_599delAGGinsCGA		non_coding_transcript_exon	Exon 4 of 4

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
PhyloP100		3.1

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr1-93730414;