rs12137697

Positions:

• chr1-111327326-G-T

Variant summary

Our verdict is Benign. Variant got -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

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
CIMAP3	XM_005270472.2	c.169+2443G>T		intron_variant			XP_005270529.1
CIMAP3	XM_017000322.2	c.169+2443G>T		intron_variant			XP_016855811.1
		n.111327326G>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.162

Gnomad4 AMR AF: 0.0998

Gnomad4 ASJ AF: 0.0901

Gnomad4 EAS AF: 0.0120

Gnomad4 SAS AF: 0.136

Gnomad4 FIN AF: 0.141

Gnomad4 NFE AF: 0.144

Gnomad4 OTH AF: 0.129

Alfa AF: 0.137 Hom.: 1810

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12137697; hg19: chr1-111869948;