22-41822852-A-C

Variant names:

• chr22-41822852-A-C
• rs7364180
• NM_024821.5:c.565-2846A>C

Variant summary

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

The NM_024821.5(CCDC134):​c.565-2846A>C 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: CCDC134 NM_024821.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.242
• Publications: 28 publications found

Genes affected

CCDC134 (HGNC:26185): (coiled-coil domain containing 134) Predicted to act upstream of or within angiogenesis and animal organ development. Located in membrane. [provided by Alliance of Genome Resources, Apr 2022]

CCDC134 Gene-Disease associations (from GenCC):

• osteogenesis imperfecta

  Inheritance: AR Classification: LIMITED Submitted by: Ambry Genetics
• osteogenesis imperfecta, IIA 22

  Inheritance: Unknown, AR Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics

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=-0.8).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024821.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC134	NM_024821.5	MANE Select	c.565-2846A>C		intron	N/A	NP_079097.1
	CCDC134	NM_001382346.1		c.565-2846A>C		intron	N/A	NP_001369275.1
	CCDC134	NM_001304797.2		c.226-2846A>C		intron	N/A	NP_001291726.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC134	ENST00000255784.6	TSL:1 MANE Select	c.565-2846A>C		intron	N/A	ENSP00000255784.5
	CCDC134	ENST00000402061.8	TSL:2	c.226-2846A>C		intron	N/A	ENSP00000385803.3

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

Alfa AF: 0.00 Hom.: 24044

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.9
DANN	Benign	0.88
PhyloP100		0.24

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: rs7364180; hg19: chr22-42218856;