1-111327326-G-T

Variant names:

• chr1-111327326-G-T
• rs12137697
• XM_005270472.2:c.169+2443G>T

Variant summary

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

The XM_005270472.2(CIMAP3):​c.169+2443G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.138 in 151,926 control chromosomes in the GnomAD database, including 1,532 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 0.14 (1532 hom., cov: 31)
• Consequence: CIMAP3 XM_005270472.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.171
• Publications: 5 publications found

Genes affected

CIMAP3 (HGNC:27009): (ciliary microtubule associated protein 3) Enables cytoskeletal protein binding activity and enzyme binding activity. Involved in positive regulation of kinase activity. Predicted to be located in trans-Golgi network. Predicted to be active in ciliary basal body. [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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.159 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.138 AC: 20973 AN: 151808 Hom.: 1534 Cov.: 31

Gnomad AFR AF: 0.162

Gnomad AMI AF: 0.113

Gnomad AMR AF: 0.0999

Gnomad ASJ AF: 0.0901

Gnomad EAS AF: 0.0117

Gnomad SAS AF: 0.136

Gnomad FIN AF: 0.141

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.144

Gnomad OTH AF: 0.130

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

GnomAD4 genome AF: 0.138 AC: 20988 AN: 151926 Hom.: 1532 Cov.: 31 AF XY: 0.137 AC XY: 10151 AN XY: 74288

African (AFR) AF: 0.162 AC: 6728 AN: 41422

American (AMR) AF: 0.0998 AC: 1525 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0901 AC: 312 AN: 3464

East Asian (EAS) AF: 0.0120 AC: 62 AN: 5184

South Asian (SAS) AF: 0.136 AC: 652 AN: 4810

European-Finnish (FIN) AF: 0.141 AC: 1483 AN: 10538

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.144 AC: 9809 AN: 67916

Other (OTH) AF: 0.129 AC: 273 AN: 2110

Alfa AF: 0.136 Hom.: 2200

Bravo AF: 0.132

Asia WGS AF: 0.0940 AC: 329 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.9
DANN	Benign	0.62
PhyloP100		0.17

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs12137697; hg19: chr1-111869948;