1-111326865-C-A

Variant names:

• chr1-111326865-C-A
• rs10776724
• XM_005270472.2:c.169+1982C>A

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+1982C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.484 in 151,950 control chromosomes in the GnomAD database, including 18,074 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 0.48 (18074 hom., cov: 32)
• Consequence: CIMAP3 XM_005270472.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.35
• Publications: 8 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=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.522 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CIMAP3	XM_005270472.2	c.169+1982C>A		intron_variant	Intron 1 of 5		XP_005270529.1
CIMAP3	XM_017000322.2	c.169+1982C>A		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: 0.484 AC: 73496 AN: 151832 Hom.: 18062 Cov.: 32

Gnomad AFR AF: 0.481

Gnomad AMI AF: 0.638

Gnomad AMR AF: 0.352

Gnomad ASJ AF: 0.590

Gnomad EAS AF: 0.434

Gnomad SAS AF: 0.539

Gnomad FIN AF: 0.492

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.507

Gnomad OTH AF: 0.473

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

GnomAD4 genome AF: 0.484 AC: 73552 AN: 151950 Hom.: 18074 Cov.: 32 AF XY: 0.482 AC XY: 35777 AN XY: 74274

African (AFR) AF: 0.481 AC: 19948 AN: 41452

American (AMR) AF: 0.351 AC: 5363 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.590 AC: 2045 AN: 3466

East Asian (EAS) AF: 0.433 AC: 2243 AN: 5176

South Asian (SAS) AF: 0.540 AC: 2599 AN: 4816

European-Finnish (FIN) AF: 0.492 AC: 5185 AN: 10540

Middle Eastern (MID) AF: 0.537 AC: 158 AN: 294

European-Non Finnish (NFE) AF: 0.507 AC: 34436 AN: 67924

Other (OTH) AF: 0.471 AC: 994 AN: 2112

Alfa AF: 0.504 Hom.: 56789

Bravo AF: 0.470

Asia WGS AF: 0.445 AC: 1548 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.22
DANN	Benign	0.52
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs10776724; hg19: chr1-111869487;