rs10776724

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.

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: 0.484 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 v4.9

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;