rs10509157

Variant names:

• chr10-61707570-C-T
• rs10509157
• NM_001366906.2:c.552+16949C>T

Variant summary

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

The NM_001366906.2(CABCOCO1):​c.552+16949C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.118 in 152,122 control chromosomes in the GnomAD database, including 1,401 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 0.12 (1401 hom., cov: 31)
• Consequence: CABCOCO1 NM_001366906.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0830
• 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]

LINC02625 (HGNC:54104): (long intergenic non-protein coding RNA 2625)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.186 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.552+16949C>T		intron	N/A	NP_001353835.1
	CABCOCO1	NM_001366908.2		c.414+16949C>T		intron	N/A	NP_001353837.1
	CABCOCO1	NM_001366905.2		c.288+16949C>T		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.552+16949C>T		intron	N/A	ENSP00000496918.2
	CABCOCO1	ENST00000330194.2	TSL:1	c.288+16949C>T		intron	N/A	ENSP00000328698.2
	LINC02625	ENST00000717515.1		n.74-22414G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.118 AC: 17922 AN: 152004 Hom.: 1393 Cov.: 31

Gnomad AFR AF: 0.190

Gnomad AMI AF: 0.0285

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.0441

Gnomad EAS AF: 0.186

Gnomad SAS AF: 0.112

Gnomad FIN AF: 0.118

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.0610

Gnomad OTH AF: 0.111

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

GnomAD4 genome AF: 0.118 AC: 17965 AN: 152122 Hom.: 1401 Cov.: 31 AF XY: 0.122 AC XY: 9046 AN XY: 74386

African (AFR) AF: 0.190 AC: 7865 AN: 41484

American (AMR) AF: 0.180 AC: 2743 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0441 AC: 153 AN: 3470

East Asian (EAS) AF: 0.187 AC: 965 AN: 5166

South Asian (SAS) AF: 0.112 AC: 541 AN: 4820

European-Finnish (FIN) AF: 0.118 AC: 1254 AN: 10594

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.0609 AC: 4144 AN: 67994

Other (OTH) AF: 0.112 AC: 236 AN: 2110

Alfa AF: 0.0934 Hom.: 94

Bravo AF: 0.124

Asia WGS AF: 0.142 AC: 492 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.4
DANN	Benign	0.71
PhyloP100		0.083
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: rs10509157; hg19: chr10-63467328;