10-61707795-G-C

Variant names:

• chr10-61707795-G-C
• rs4590817
• NM_001366906.2:c.552+17174G>C

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+17174G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.145 in 151,956 control chromosomes in the GnomAD database, including 1,716 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 0.14 (1716 hom., cov: 31)
• Consequence: CABCOCO1 NM_001366906.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.19
• Publications: 43 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.159 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CABCOCO1	NM_001366906.2	c.552+17174G>C		intron_variant	Intron 5 of 7	ENST00000648843.3	NP_001353835.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CABCOCO1	ENST00000648843.3	c.552+17174G>C		intron_variant	Intron 5 of 7		NM_001366906.2	ENSP00000496918.2

Frequencies

GnomAD3 genomes AF: 0.145 AC: 21951 AN: 151838 Hom.: 1714 Cov.: 31

Gnomad AFR AF: 0.162

Gnomad AMI AF: 0.132

Gnomad AMR AF: 0.0990

Gnomad ASJ AF: 0.217

Gnomad EAS AF: 0.000963

Gnomad SAS AF: 0.0810

Gnomad FIN AF: 0.111

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.160

Gnomad OTH AF: 0.159

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

GnomAD4 genome AF: 0.145 AC: 21973 AN: 151956 Hom.: 1716 Cov.: 31 AF XY: 0.140 AC XY: 10426 AN XY: 74264

African (AFR) AF: 0.162 AC: 6722 AN: 41400

American (AMR) AF: 0.0987 AC: 1504 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.217 AC: 753 AN: 3468

East Asian (EAS) AF: 0.000965 AC: 5 AN: 5180

South Asian (SAS) AF: 0.0806 AC: 389 AN: 4826

European-Finnish (FIN) AF: 0.111 AC: 1176 AN: 10568

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.160 AC: 10900 AN: 67962

Other (OTH) AF: 0.161 AC: 340 AN: 2114

Alfa AF: 0.159 Hom.: 1142

Bravo AF: 0.147

Asia WGS AF: 0.0660 AC: 233 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.11
DANN	Benign	0.46
PhyloP100		-2.2
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: rs4590817; hg19: chr10-63467553;