chr10-32451877-C-T

Position:

• chr10-32451877-C-T

Variant summary

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

The NM_001395015.1(CCDC7):​c.235C>T​(p.Pro79Ser) 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: 32)
• Consequence: CCDC7 NM_001395015.1 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 0.119

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=0.02785927).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CCDC7	NM_001395015.1	c.235C>T	p.Pro79Ser	missense_variant	2/44	ENST00000639629.2	NP_001381944.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCDC7	ENST00000639629.2	c.235C>T	p.Pro79Ser	missense_variant	2/44	5	NM_001395015.1	ENSP00000491655.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Jul 05, 2024

The c.235C>T (p.P79S) alteration is located in exon 2 (coding exon 1) of the CCDC7 gene. This alteration results from a C to T substitution at nucleotide position 235, causing the proline (P) at amino acid position 79 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.16
BayesDel_addAF	Benign	-0.35	T
BayesDel_noAF	Benign	-0.74
CADD	Benign	0.63
DANN	Benign	0.30
DEOGEN2	Benign	0.0033	.;.;T;T;T;.
Eigen	Benign	-1.6
Eigen_PC	Benign	-1.6
FATHMM_MKL	Benign	0.0086	N
LIST_S2	Benign	0.61	.;T;T;T;T;T
M_CAP	Benign	0.0015	T
MetaRNN	Benign	0.028	T;T;T;T;T;T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	-0.46	N;N;.;.;.;N
PrimateAI	Benign	0.34	T
PROVEAN	Benign	1.5	N;N;N;N;N;.
REVEL	Benign	0.032
Sift	Benign	1.0	T;T;T;T;T;.
Sift4G	Benign	0.68	T;T;T;T;T;.
Polyphen		0.0	.;.;B;.;.;B
Vest4		0.11
MutPred		0.17		Gain of phosphorylation at P79 (P = 0.085);Gain of phosphorylation at P79 (P = 0.085);Gain of phosphorylation at P79 (P = 0.085);Gain of phosphorylation at P79 (P = 0.085);Gain of phosphorylation at P79 (P = 0.085);Gain of phosphorylation at P79 (P = 0.085);
MVP		0.10
MPC		0.061
ClinPred		0.059	T
GERP RS		-2.8
Varity_R		0.022
gMVP		0.0082

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.12		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: chr10-32740805;