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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CIMAP3	XM_005270472.2	c.169+2443G>T		intron_variant	Intron 1 of 5		XP_005270529.1
CIMAP3	XM_017000322.2	c.169+2443G>T		intron_variant	Intron 1 of 4		XP_016855811.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;