rs994811

Variant names:

• chr10-61735126-T-C
• rs994811
• NM_001366906.2:c.553-24933T>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.553-24933T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.42 in 151,804 control chromosomes in the GnomAD database, including 15,610 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 0.42 (15610 hom., cov: 31)
• Consequence: CABCOCO1 NM_001366906.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0910
• Publications: 2 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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.543 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CABCOCO1	NM_001366906.2	c.553-24933T>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.553-24933T>C		intron_variant	Intron 5 of 7		NM_001366906.2	ENSP00000496918.2

Frequencies

GnomAD3 genomes AF: 0.420 AC: 63715 AN: 151686 Hom.: 15603 Cov.: 31

Gnomad AFR AF: 0.170

Gnomad AMI AF: 0.572

Gnomad AMR AF: 0.490

Gnomad ASJ AF: 0.538

Gnomad EAS AF: 0.164

Gnomad SAS AF: 0.479

Gnomad FIN AF: 0.513

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.547

Gnomad OTH AF: 0.464

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

GnomAD4 genome AF: 0.420 AC: 63737 AN: 151804 Hom.: 15610 Cov.: 31 AF XY: 0.421 AC XY: 31242 AN XY: 74194

African (AFR) AF: 0.170 AC: 7062 AN: 41442

American (AMR) AF: 0.490 AC: 7453 AN: 15206

Ashkenazi Jewish (ASJ) AF: 0.538 AC: 1864 AN: 3462

East Asian (EAS) AF: 0.163 AC: 843 AN: 5156

South Asian (SAS) AF: 0.480 AC: 2311 AN: 4814

European-Finnish (FIN) AF: 0.513 AC: 5401 AN: 10538

Middle Eastern (MID) AF: 0.537 AC: 158 AN: 294

European-Non Finnish (NFE) AF: 0.547 AC: 37148 AN: 67872

Other (OTH) AF: 0.463 AC: 975 AN: 2108

Alfa AF: 0.485 Hom.: 7171

Bravo AF: 0.407

Asia WGS AF: 0.317 AC: 1099 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.7
DANN	Benign	0.58
PhyloP100		0.091
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: rs994811; hg19: chr10-63494884;