chr22-36999870-C-G

Variant names:

• chr22-36999870-C-G
• NM_001163857.2:c.604G>C

Variant summary

Our verdict is Uncertain significance. The variant received 3 ACMG points: 3P and 0B. PM2 PP3

The NM_001163857.2(CIMIP4):​c.604G>C​(p.Gly202Arg) 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. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 29)
• Consequence: CIMIP4 NM_001163857.2 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 2.76
• Publications: 0 publications found

Genes affected

CIMIP4 (HGNC:28568): (ciliary microtubule inner protein 4)

ACMG classification

Our verdict: Uncertain_significance. The variant received 3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.794

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001163857.2. 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
	CIMIP4	NM_001163857.2	MANE Select	c.604G>C	p.Gly202Arg	missense	Exon 4 of 6	NP_001157329.1	O43247-1
	CIMIP4	NM_178552.4		c.349G>C	p.Gly117Arg	missense	Exon 4 of 6	NP_848647.1	O43247-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CIMIP4	ENST00000381821.2	TSL:1 MANE Select	c.604G>C	p.Gly202Arg	missense	Exon 4 of 6	ENSP00000371243.1	O43247-1
	CIMIP4	ENST00000402860.7	TSL:1	c.349G>C	p.Gly117Arg	missense	Exon 4 of 6	ENSP00000385179.3	O43247-2
	CIMIP4	ENST00000405091.6	TSL:5	c.604G>C	p.Gly202Arg	missense	Exon 5 of 7	ENSP00000386118.2	O43247-1

Frequencies

GnomAD3 genomes Cov.: 29

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 29

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	1	-	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.96
BayesDel_addAF	Pathogenic	0.37	D
BayesDel_noAF	Pathogenic	0.30
CADD	Uncertain	23
DANN	Uncertain	0.99
DEOGEN2	Benign	0.13	T
Eigen	Benign	0.036
Eigen_PC	Benign	0.082
FATHMM_MKL	Benign	0.68	D
LIST_S2	Benign	0.86	D
M_CAP	Benign	0.011	T
MetaRNN	Pathogenic	0.79	D
MetaSVM	Benign	-0.91	T
MutationAssessor	Uncertain	2.7	M
PhyloP100		2.8
PrimateAI	Uncertain	0.69	T
PROVEAN	Pathogenic	-6.0	D
REVEL	Uncertain	0.53
Sift	Uncertain	0.0070	D
Sift4G	Uncertain	0.0070	D
Polyphen		1.0	D
Vest4		0.95
MutPred		0.57		Gain of solvent accessibility (P = 0.0171)
MVP		0.13
MPC		0.037
ClinPred		0.98	D
GERP RS		3.8
Varity_R		0.38
gMVP		0.30
Mutation Taster		=78/22	polymorphism

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

hg19: chr22-37395911;