rs12765373

Positions:

• chr10-61672290-T-A

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CABCOCO1	NM_001366906.2	c.61-342T>A		intron_variant		ENST00000648843.3	NP_001353835.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CABCOCO1	ENST00000648843.3	c.61-342T>A		intron_variant			NM_001366906.2	ENSP00000496918
CABCOCO1	ENST00000330194.2	c.-100-8853T>A		intron_variant		1		ENSP00000328698	P1
CABCOCO1	ENST00000389639.3	c.-9+9258T>A		intron_variant		5		ENSP00000374290

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

Gnomad4 AFR AF: 0.188

Gnomad4 AMR AF: 0.189

Gnomad4 ASJ AF: 0.0586

Gnomad4 EAS AF: 0.232

Gnomad4 SAS AF: 0.135

Gnomad4 FIN AF: 0.165

Gnomad4 NFE AF: 0.0779

Gnomad4 OTH AF: 0.120

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	1.4
DANN	Benign	0.82

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

Publications

LitVar

Other links and lift over

dbSNP: rs12765373; hg19: chr10-63432048;