15-75727323-C-G

Variant names:

• chr15-75727323-C-G
• rs771060062
• NM_175881.5:c.608C>G

Variant summary

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

The NM_175881.5(CIMAP1C):​c.608C>G​(p.Thr203Arg) 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. T203M) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 32)
• Consequence: CIMAP1C NM_175881.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.88
• Publications: 0 publications found

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

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 (MetaRNN=0.035137177).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_175881.5. 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
	CIMAP1C	NM_175881.5	MANE Select	c.608C>G	p.Thr203Arg	missense	Exon 4 of 4	NP_787077.1	Q8IXM7

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CIMAP1C	ENST00000332145.3	TSL:1 MANE Select	c.608C>G	p.Thr203Arg	missense	Exon 4 of 4	ENSP00000329584.2	Q8IXM7

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.078
BayesDel_addAF	Benign	-0.36	T
BayesDel_noAF	Benign	-0.76
CADD	Benign	0.0010
DANN	Benign	0.50
DEOGEN2	Benign	0.0017	T
Eigen	Benign	-2.4
Eigen_PC	Benign	-2.5
FATHMM_MKL	Benign	0.0055	N
LIST_S2	Benign	0.36	T
M_CAP	Benign	0.0032	T
MetaRNN	Benign	0.035	T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	-0.20	N
PhyloP100		-3.9
PrimateAI	Benign	0.22	T
PROVEAN	Benign	1.3	N
REVEL	Benign	0.038
Sift	Benign	1.0	T
Sift4G	Benign	0.80	T
Polyphen		0.0050	B
Vest4		0.15
MutPred		0.44		Loss of phosphorylation at T203 (P = 0.0206)
MVP		0.014
MPC		0.33
ClinPred		0.087	T
GERP RS		-9.3
Varity_R		0.067
gMVP		0.59

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs771060062; hg19: chr15-76019664;