rs1530440

Variant names:

• chr10-61764833-C-T
• rs1530440
• NM_001366906.2:c.817-1106C>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.817-1106C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.153 in 152,050 control chromosomes in the GnomAD database, including 2,054 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 0.15 (2054 hom., cov: 31)
• Consequence: CABCOCO1 NM_001366906.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.300
• Publications: 56 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=-0.82).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.2 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CABCOCO1	NM_001366906.2	MANE Select	c.817-1106C>T		intron	N/A	NP_001353835.1	A0A7I2UT39
	CABCOCO1	NM_001366908.2		c.679-1106C>T		intron	N/A	NP_001353837.1
	CABCOCO1	NM_001366905.2		c.553-1106C>T		intron	N/A	NP_001353834.1	Q8IVU9

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CABCOCO1	ENST00000648843.3	MANE Select	c.817-1106C>T		intron	N/A	ENSP00000496918.2	A0A7I2UT39
	CABCOCO1	ENST00000330194.2	TSL:1	c.553-1106C>T		intron	N/A	ENSP00000328698.2	Q8IVU9
	CABCOCO1	ENST00000941429.1		c.694-1106C>T		intron	N/A	ENSP00000611488.1

Frequencies

GnomAD3 genomes AF: 0.153 AC: 23182 AN: 151932 Hom.: 2049 Cov.: 31

Gnomad AFR AF: 0.0606

Gnomad AMI AF: 0.120

Gnomad AMR AF: 0.205

Gnomad ASJ AF: 0.227

Gnomad EAS AF: 0.186

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.192

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.184

Gnomad OTH AF: 0.170

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

GnomAD4 genome AF: 0.153 AC: 23191 AN: 152050 Hom.: 2054 Cov.: 31 AF XY: 0.153 AC XY: 11396 AN XY: 74328

African (AFR) AF: 0.0605 AC: 2510 AN: 41490

American (AMR) AF: 0.206 AC: 3142 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.227 AC: 787 AN: 3472

East Asian (EAS) AF: 0.186 AC: 962 AN: 5170

South Asian (SAS) AF: 0.149 AC: 718 AN: 4818

European-Finnish (FIN) AF: 0.192 AC: 2035 AN: 10574

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.184 AC: 12496 AN: 67960

Other (OTH) AF: 0.171 AC: 361 AN: 2112

Alfa AF: 0.174 Hom.: 7393

Bravo AF: 0.150

Asia WGS AF: 0.156 AC: 546 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.98
DANN	Benign	0.48
PhyloP100		-0.30
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs1530440; hg19: chr10-63524591;