rs752600669

Variant names:

• chr15-75726136-C-A
• rs752600669
• NM_175881.5:c.308C>A

Your query was ambiguous. Multiple possible variants found:

• chr15-75726136-C-A
• chr15-75726136-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2 PP3_Moderate

The NM_175881.5(CIMAP1C):​c.308C>A​(p.Pro103Gln) 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 pathogenic 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. P103L) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 33)
• Consequence: CIMAP1C NM_175881.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.13

Genes affected

CIMAP1C (HGNC:28735): (ciliary microtubule associated protein 1C) Predicted to be active in cytoskeleton. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Uncertain_significance. Variant got 4 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.901

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CIMAP1C	NM_175881.5	c.308C>A	p.Pro103Gln	missense_variant	Exon 3 of 4	ENST00000332145.3	NP_787077.1
CIMAP1C	XM_006720414.4	c.359C>A	p.Pro120Gln	missense_variant	Exon 3 of 4		XP_006720477.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ODF3L1	ENST00000332145.3	c.308C>A	p.Pro103Gln	missense_variant	Exon 3 of 4	1	NM_175881.5	ENSP00000329584.2

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 33

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.16
BayesDel_addAF	Benign	-0.021	T
BayesDel_noAF	Benign	-0.27
CADD	Benign	23
DANN	Uncertain	0.99
DEOGEN2	Benign	0.36	T
Eigen	Uncertain	0.67
Eigen_PC	Uncertain	0.62
FATHMM_MKL	Uncertain	0.88	D
LIST_S2	Benign	0.66	T
M_CAP	Benign	0.034	D
MetaRNN	Pathogenic	0.90	D
MetaSVM	Benign	-0.33	T
MutationAssessor	Pathogenic	3.4	M
PrimateAI	Benign	0.36	T
PROVEAN	Pathogenic	-6.7	D
REVEL	Uncertain	0.32
Sift	Uncertain	0.0020	D
Sift4G	Uncertain	0.0030	D
Polyphen		0.99	D
Vest4		0.53
MutPred		0.83		Loss of disorder (P = 0.1526);
MVP		0.32
MPC		0.79
ClinPred		0.98	D
GERP RS		5.2
Varity_R		0.38
gMVP		0.66

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

LitVar

Other links and lift over

dbSNP: rs752600669; hg19: chr15-76018477;