22-30370477-CT-TG

Variant names:

• chr22-30370477-CT-TG
• NM_001017437.5:c.572_573delCTinsTG
• CCDC157 p.Pro191Leu

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_001017437.5(CCDC157):​c.572_573delCTinsTG​(p.Pro191Leu) variant causes a missense 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.

• Frequency: Genomes: not found (cov: 33)
• Consequence: CCDC157 NM_001017437.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.57
• Publications: 0 publications found

Genes affected

CCDC157 (HGNC:33854): (coiled-coil domain containing 157)

RNF215 (HGNC:33434): (ring finger protein 215) Predicted to enable ubiquitin protein ligase activity. Predicted to be involved in Golgi to vacuole transport; protein targeting to vacuole; and ubiquitin-dependent protein catabolic process. Predicted to be integral component of membrane. Predicted to be part of Golgi transport complex. Predicted to be active in endosome; membrane; and trans-Golgi network. [provided by Alliance of Genome Resources, Apr 2022]

KIAA1656 (HGNC:):

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001017437.5. 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
	CCDC157	NM_001017437.5	MANE Select	c.572_573delCTinsTG	p.Pro191Leu	missense	N/A	NP_001017437.3	Q569K6
	CCDC157	NM_001318334.2		c.572_573delCTinsTG	p.Pro191Leu	missense	N/A	NP_001305263.2	Q569K6
	KIAA1656	NR_046312.1		n.5938_5939delAGinsCA		non_coding_transcript_exon	Exon 2 of 2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC157	ENST00000338306.8	TSL:5 MANE Select	c.572_573delCTinsTG	p.Pro191Leu	missense	N/A	ENSP00000343087.3	Q569K6
	CCDC157	ENST00000405659.5	TSL:1	c.572_573delCTinsTG	p.Pro191Leu	missense	N/A	ENSP00000385357.1	Q569K6
	CCDC157	ENST00000430839.5	TSL:3	c.572_573delCTinsTG	p.Pro191Leu	missense	N/A	ENSP00000401837.1	E7ETG3

Frequencies

GnomAD3 genomes Cov.: 33

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

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		1.6

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: chr22-30766466;