chr9-137245095-T-C

Variant names:

• chr9-137245095-T-C
• NM_001001710.3:c.646A>G

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_001001710.3(CIMIP2A):​c.646A>G​(p.Ile216Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 33)
• Consequence: CIMIP2A NM_001001710.3 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 0.956
• Publications: 0 publications found

Genes affected

CIMIP2A (HGNC:33818): (ciliary microtubule inner protein 2A) Located in ciliary basal body. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001001710.3. 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
	CIMIP2A	NM_001001710.3	MANE Select	c.646A>G	p.Ile216Val	missense	Exon 4 of 7	NP_001001710.1	Q6J272-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CIMIP2A	ENST00000344774.6	TSL:1 MANE Select	c.646A>G	p.Ile216Val	missense	Exon 4 of 7	ENSP00000344729.4	Q6J272-1
	CIMIP2A	ENST00000471784.2	TSL:2	n.701A>G		non_coding_transcript_exon	Exon 4 of 6
	CIMIP2A	ENST00000484720.1	TSL:3	c.*57A>G		downstream_gene	N/A	ENSP00000420741.1	C9JBW9

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 37

GnomAD4 genome Cov.: 33

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	Benign	0.13
BayesDel_addAF	Benign	-0.0096	T
BayesDel_noAF	Benign	-0.25
CADD	Benign	23
DANN	Uncertain	1.0
DEOGEN2	Benign	0.035	T
Eigen	Uncertain	0.32
Eigen_PC	Uncertain	0.23
FATHMM_MKL	Benign	0.45	N
LIST_S2	Benign	0.59	T
M_CAP	Benign	0.0088	T
MetaRNN	Uncertain	0.66	D
MetaSVM	Benign	-0.67	T
MutationAssessor	Benign	1.9	L
PhyloP100		0.96
PrimateAI	Uncertain	0.51	T
PROVEAN	Benign	-0.33	N
REVEL	Benign	0.28
Sift	Benign	0.17	T
Sift4G	Pathogenic	0.0	D
Polyphen		0.98	D
Vest4		0.53
MutPred		0.78		Loss of helix (P = 0.1299)
MVP		0.12
MPC		0.011
ClinPred		0.88	D
GERP RS		5.2
Varity_R		0.043
gMVP		0.53
Mutation Taster		=93/7	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

hg19: chr9-140139547;