rs733168

Variant names:

• chr1-54816883-A-G
• rs733168
• NM_001110533.2:c.1051-106A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001110533.2(CIMAP2):​c.1051-106A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.651 in 1,417,278 control chromosomes in the GnomAD database, including 303,562 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.61 (28941 hom., cov: 31)
  • Exomes 𝑓: 0.66 (274621 hom.)
• Consequence: CIMAP2 NM_001110533.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.859
• Publications: 8 publications found

Genes affected

CIMAP2 (HGNC:26854): (ciliary microtubule associated protein 2) Predicted to enable mitochondrial ribosome binding activity. Predicted to act upstream of or within positive regulation of cell population proliferation and positive regulation of oxidative phosphorylation. Predicted to be located in mitochondrion. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.727 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001110533.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CIMAP2	NM_001110533.2	MANE Select	c.1051-106A>G		intron	N/A	NP_001104003.1
	CIMAP2	NM_152607.3		c.1051-106A>G		intron	N/A	NP_689820.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CIMAP2	ENST00000371273.4	TSL:1 MANE Select	c.1051-106A>G		intron	N/A	ENSP00000360320.3
	CIMAP2	ENST00000358193.7	TSL:1	c.1051-106A>G		intron	N/A	ENSP00000350924.3

Frequencies

GnomAD3 genomes AF: 0.611 AC: 92765 AN: 151834 Hom.: 28950 Cov.: 31

Gnomad AFR AF: 0.496

Gnomad AMI AF: 0.714

Gnomad AMR AF: 0.598

Gnomad ASJ AF: 0.640

Gnomad EAS AF: 0.437

Gnomad SAS AF: 0.749

Gnomad FIN AF: 0.738

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.665

Gnomad OTH AF: 0.606

GnomAD4 exome AF: 0.656 AC: 830080 AN: 1265324 Hom.: 274621 AF XY: 0.658 AC XY: 411010 AN XY: 624206

African (AFR) AF: 0.487 AC: 14188 AN: 29142

American (AMR) AF: 0.545 AC: 18004 AN: 33028

Ashkenazi Jewish (ASJ) AF: 0.638 AC: 13478 AN: 21114

East Asian (EAS) AF: 0.454 AC: 16601 AN: 36560

South Asian (SAS) AF: 0.736 AC: 51966 AN: 70582

European-Finnish (FIN) AF: 0.726 AC: 34295 AN: 47236

Middle Eastern (MID) AF: 0.569 AC: 2686 AN: 4724

European-Non Finnish (NFE) AF: 0.665 AC: 644875 AN: 969672

Other (OTH) AF: 0.638 AC: 33987 AN: 53266

GnomAD4 genome AF: 0.611 AC: 92786 AN: 151954 Hom.: 28941 Cov.: 31 AF XY: 0.616 AC XY: 45706 AN XY: 74252

African (AFR) AF: 0.495 AC: 20518 AN: 41426

American (AMR) AF: 0.597 AC: 9119 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.640 AC: 2221 AN: 3470

East Asian (EAS) AF: 0.437 AC: 2243 AN: 5132

South Asian (SAS) AF: 0.748 AC: 3604 AN: 4820

European-Finnish (FIN) AF: 0.738 AC: 7800 AN: 10574

Middle Eastern (MID) AF: 0.568 AC: 166 AN: 292

European-Non Finnish (NFE) AF: 0.665 AC: 45180 AN: 67940

Other (OTH) AF: 0.608 AC: 1285 AN: 2112

Alfa AF: 0.638 Hom.: 4063

Bravo AF: 0.582

Asia WGS AF: 0.584 AC: 2034 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.19
DANN	Benign	0.40
PhyloP100		-0.86
Mutation Taster		=100/0	polymorphism (auto)

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: rs733168; hg19: chr1-55282556; COSMIC: COSV64022882;