10-32518443-C-G

Position:

• chr10-32518443-C-G

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001395015.1(CCDC7):​c.931C>G​(p.Gln311Glu) variant causes a missense 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. 15/21 in silico tools predict 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: 33)
• Consequence: CCDC7 NM_001395015.1 missense
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.328

Genes affected

CCDC7 (HGNC:26533): (coiled-coil domain containing 7)

CCDC7 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.03254512).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CCDC7	NM_001395015.1	c.931C>G	p.Gln311Glu	missense_variant	12/44	ENST00000639629.2	NP_001381944.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCDC7	ENST00000639629.2	c.931C>G	p.Gln311Glu	missense_variant	12/44	5	NM_001395015.1	ENSP00000491655.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 33

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Ambry Genetics

Oct 08, 2024

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.090
BayesDel_addAF	Benign	-0.36	T
BayesDel_noAF	Benign	-0.75
CADD	Benign	0.075
DANN	Benign	0.085
Eigen	Benign	-1.6
Eigen_PC	Benign	-1.6
FATHMM_MKL	Benign	0.011	N
LIST_S2	Benign	0.55	.;T;T
M_CAP	Benign	0.0013	T
MetaRNN	Benign	0.033	T;T;T
MetaSVM	Benign	-0.98	T
MutationAssessor	Benign	-0.17	N;N;N
PrimateAI	Benign	0.46	T
PROVEAN	Benign	0.10	N;N;.
REVEL	Benign	0.013
Sift	Benign	0.83	T;T;.
Sift4G	Benign	1.0	T;T;.
Polyphen		0.0	.;.;B
Vest4		0.22
MutPred		0.19		Gain of phosphorylation at S314 (P = 0.0928);Gain of phosphorylation at S314 (P = 0.0928);Gain of phosphorylation at S314 (P = 0.0928);
MVP		0.17
MPC		0.063
ClinPred		0.031	T
GERP RS		-2.1
Varity_R		0.035
gMVP		0.0064

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr10-32807371;