rs12765373

Variant names:

• chr10-61672290-T-A
• rs12765373
• NM_001366906.2:c.61-342T>A

Variant summary

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

The NM_001366906.2(CABCOCO1):​c.61-342T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.132 in 152,234 control chromosomes in the GnomAD database, including 1,651 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 0.13 (1651 hom., cov: 32)
• Consequence: CABCOCO1 NM_001366906.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0440
• Publications: 4 publications found

Genes affected

CABCOCO1 (HGNC:28678): (ciliary associated calcium binding coiled-coil 1) Predicted to enable calcium ion binding activity. Predicted to be located in centrosome; cytoplasm; and sperm flagellum. [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=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.221 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001366906.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CABCOCO1	NM_001366906.2	MANE Select	c.61-342T>A		intron	N/A	NP_001353835.1
	CABCOCO1	NM_001366908.2		c.-78-342T>A		intron	N/A	NP_001353837.1
	CABCOCO1	NM_001366905.2		c.-100-8853T>A		intron	N/A	NP_001353834.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CABCOCO1	ENST00000648843.3	MANE Select	c.61-342T>A		intron	N/A	ENSP00000496918.2
	CABCOCO1	ENST00000330194.2	TSL:1	c.-100-8853T>A		intron	N/A	ENSP00000328698.2
	CABCOCO1	ENST00000389639.3	TSL:5	c.-9+9258T>A		intron	N/A	ENSP00000374290.4

Frequencies

GnomAD3 genomes AF: 0.132 AC: 20099 AN: 152116 Hom.: 1643 Cov.: 32

Gnomad AFR AF: 0.188

Gnomad AMI AF: 0.0592

Gnomad AMR AF: 0.188

Gnomad ASJ AF: 0.0586

Gnomad EAS AF: 0.232

Gnomad SAS AF: 0.134

Gnomad FIN AF: 0.165

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.0779

Gnomad OTH AF: 0.119

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

GnomAD4 genome AF: 0.132 AC: 20143 AN: 152234 Hom.: 1651 Cov.: 32 AF XY: 0.137 AC XY: 10217 AN XY: 74444

African (AFR) AF: 0.188 AC: 7810 AN: 41524

American (AMR) AF: 0.189 AC: 2888 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0586 AC: 203 AN: 3464

East Asian (EAS) AF: 0.232 AC: 1200 AN: 5178

South Asian (SAS) AF: 0.135 AC: 651 AN: 4826

European-Finnish (FIN) AF: 0.165 AC: 1746 AN: 10608

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.0779 AC: 5298 AN: 68012

Other (OTH) AF: 0.120 AC: 254 AN: 2114

Alfa AF: 0.106 Hom.: 105

Bravo AF: 0.135

Asia WGS AF: 0.178 AC: 619 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	1.4
DANN	Benign	0.82
PhyloP100		0.044
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.050		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs12765373; hg19: chr10-63432048;