rs915560320

Variant names:

• chr9-36170031-C-G
• rs915560320
• NM_005893.3:c.529C>G

Your query was ambiguous. Multiple possible variants found:

• chr9-36170031-C-G
• chr9-36170031-C-T

Variant summary

Our verdict is Uncertain significance. The variant received 1 ACMG points: 3P and 2B. PM2 PP2 BP4_Moderate

The NM_005893.3(CCIN):​c.529C>G​(p.Pro177Ala) 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. 16/22 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P177S) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 33)
• Consequence: CCIN NM_005893.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.59
• Publications: 0 publications found

Genes affected

CCIN (HGNC:1568): (calicin) The protein encoded by this gene is a basic protein of the sperm head cytoskeleton. This protein contains kelch repeats and a BTB/POZ domain and is necessary for normal morphology during sperm differentiation. This gene is intronless. [provided by RefSeq, Jul 2008]

ENSG00000295960 (HGNC:):

ACMG classification

Our verdict: Uncertain_significance. The variant received 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP2: Missense variant in the gene, where a lot of missense mutations are associated with disease in ClinVar. The gene has 4 curated pathogenic missense variants (we use a threshold of 10). The gene has 1 curated benign missense variants. Gene score misZ: 1.2971 (below the threshold of 3.09). Trascript score misZ: 2.2447 (below the threshold of 3.09).
• BP4: Computational evidence support a benign effect (MetaRNN=0.09357181).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005893.3. 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
	CCIN	NM_005893.3	MANE Select	c.529C>G	p.Pro177Ala	missense	Exon 1 of 1	NP_005884.2	Q13939

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCIN	ENST00000335119.4	TSL:6 MANE Select	c.529C>G	p.Pro177Ala	missense	Exon 1 of 1	ENSP00000334996.2	Q13939
	ENSG00000295960	ENST00000734529.1		n.78-1954G>C		intron	N/A

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 34

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.11
BayesDel_addAF	Benign	-0.074	T
BayesDel_noAF	Benign	-0.34
CADD	Benign	18
DANN	Benign	0.17
DEOGEN2	Benign	0.033	T
Eigen	Benign	-0.60
Eigen_PC	Benign	-0.46
FATHMM_MKL	Benign	0.13	N
LIST_S2	Benign	0.63	T
M_CAP	Benign	0.030	D
MetaRNN	Benign	0.094	T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	0.34	N
PhyloP100		1.6
PrimateAI	Uncertain	0.51	T
PROVEAN	Benign	1.8	N
REVEL	Benign	0.15
Sift	Benign	0.62	T
Sift4G	Benign	0.57	T
Polyphen		0.0040	B
Vest4		0.24
MutPred		0.61		Loss of catalytic residue at P176 (P = 0.0571)
MVP		0.56
MPC		0.27
ClinPred		0.072	T
GERP RS		4.6
Varity_R		0.059
gMVP		0.40
Mutation Taster		=79/21	polymorphism

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: rs915560320; hg19: chr9-36170028;