1-54817403-T-G

Variant names:

• chr1-54817403-T-G
• rs4926658
• NM_001110533.2:c.1184+281T>G

Variant summary

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

The ENST00000371273.4(CIMAP2):​c.1184+281T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.611 in 152,042 control chromosomes in the GnomAD database, including 28,952 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as (no stars).

• Frequency: Genomes: 𝑓 0.61 (28952 hom., cov: 32)
• Consequence: CIMAP2 ENST00000371273.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.704
• Publications: 5 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=-0.9).
• 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: ENST00000371273.4. 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.1184+281T>G		intron	N/A	NP_001104003.1
	CIMAP2	NM_152607.3		c.1184+281T>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.1184+281T>G		intron	N/A	ENSP00000360320.3
	CIMAP2	ENST00000358193.7	TSL:1	c.1184+281T>G		intron	N/A	ENSP00000350924.3

Frequencies

GnomAD3 genomes AF: 0.611 AC: 92803 AN: 151924 Hom.: 28961 Cov.: 32

Gnomad AFR AF: 0.496

Gnomad AMI AF: 0.715

Gnomad AMR AF: 0.598

Gnomad ASJ AF: 0.640

Gnomad EAS AF: 0.435

Gnomad SAS AF: 0.748

Gnomad FIN AF: 0.738

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.665

Gnomad OTH AF: 0.606

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.611 AC: 92824 AN: 152042 Hom.: 28952 Cov.: 32 AF XY: 0.615 AC XY: 45731 AN XY: 74324

African (AFR) AF: 0.495 AC: 20519 AN: 41444

American (AMR) AF: 0.597 AC: 9128 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.640 AC: 2218 AN: 3464

East Asian (EAS) AF: 0.436 AC: 2250 AN: 5164

South Asian (SAS) AF: 0.748 AC: 3596 AN: 4810

European-Finnish (FIN) AF: 0.738 AC: 7801 AN: 10574

Middle Eastern (MID) AF: 0.565 AC: 166 AN: 294

European-Non Finnish (NFE) AF: 0.665 AC: 45206 AN: 67976

Other (OTH) AF: 0.609 AC: 1289 AN: 2116

Alfa AF: 0.639 Hom.: 16167

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	-0.90
CADD	Benign	4.8
DANN	Benign	0.62
PhyloP100		-0.70
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs4926658; hg19: chr1-55283076;