chr14-57480680-G-A

Variant names:

• chr14-57480680-G-A
• NM_018168.4:c.570C>T
• CCDC198 p.Ala190Ala

Variant summary

Our verdict is Likely benign. The variant received -1 ACMG points: 2P and 3B. PM2 BP4_Moderate BP7

The NM_018168.4(CCDC198):​c.570C>T​(p.Ala190Ala) variant causes a synonymous 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: CCDC198 NM_018168.4 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.278
• Publications: 0 publications found

Genes affected

CCDC198 (HGNC:20189): (coiled-coil domain containing 198)

ACMG classification

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

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (REVEL=0.018).
• BP7: Synonymous conserved (PhyloP=-0.278 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018168.4. 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
	CCDC198	NM_018168.4	MANE Select	c.570C>T	p.Ala190Ala	synonymous	Exon 5 of 6	NP_060638.2	Q9NVL8
	CCDC198	NM_001283056.2		c.567C>T	p.Ala189Ala	synonymous	Exon 5 of 7	NP_001269985.1	F5GWJ3
	CCDC198	NM_001283057.2		c.567C>T	p.Ala189Ala	synonymous	Exon 5 of 6	NP_001269986.1	E9PSE9

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC198	ENST00000216445.8	TSL:1 MANE Select	c.570C>T	p.Ala190Ala	synonymous	Exon 5 of 6	ENSP00000216445.3	Q9NVL8
	CCDC198	ENST00000422976.6	TSL:1	c.567C>T	p.Ala189Ala	synonymous	Exon 5 of 7	ENSP00000392368.2	F5GWJ3
	CCDC198	ENST00000534126.5	TSL:1	c.567C>T	p.Ala189Ala	synonymous	Exon 5 of 6	ENSP00000434003.1	E9PSE9

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	1.8
DANN	Benign	0.45
PhyloP100		-0.28

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

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

Other links and lift over

hg19: chr14-57947398;