1-16889836-C-A

Variant names:

• chr1-16889836-C-A
• rs6586513
• ENST00000466256.6:n.126-40450C>A

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000466256.6(CROCC):​n.126-40450C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.71 (33684 hom., cov: 44)
  • Failed GnomAD Quality Control
• Consequence: CROCC ENST00000466256.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -6.05
• Publications: 12 publications found

Genes affected

CROCC (HGNC:21299): (ciliary rootlet coiled-coil, rootletin) Predicted to enable kinesin binding activity and structural molecule activity. Involved in several processes, including centriole-centriole cohesion; positive regulation of cilium assembly; and positive regulation of protein localization to cilium. Located in cytoskeleton; cytosol; and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000302843 (HGNC:):

TRN-GTT4-1 (HGNC:33197):

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000466256.6. 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
	LOC105376805	NR_135058.1		n.-170G>T		upstream_gene	N/A
	LOC105376805	NR_135059.1		n.-170G>T		upstream_gene	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CROCC	ENST00000466256.6	TSL:5	n.126-40450C>A		intron	N/A
	ENSG00000302843	ENST00000789963.1		n.374-17808C>A		intron	N/A
	ENSG00000238142	ENST00000790083.1		n.95-233G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.712 AC: 107595 AN: 151136 Hom.: 33688 Cov.: 44

Gnomad AFR AF: 0.598

Gnomad AMI AF: 0.788

Gnomad AMR AF: 0.725

Gnomad ASJ AF: 0.770

Gnomad EAS AF: 0.853

Gnomad SAS AF: 0.740

Gnomad FIN AF: 0.719

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.759

Gnomad OTH AF: 0.729

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.712 AC: 107642 AN: 151252 Hom.: 33684 Cov.: 44 AF XY: 0.714 AC XY: 52786 AN XY: 73942

African (AFR) AF: 0.598 AC: 24418 AN: 40830

American (AMR) AF: 0.725 AC: 11042 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.770 AC: 2669 AN: 3464

East Asian (EAS) AF: 0.852 AC: 4421 AN: 5186

South Asian (SAS) AF: 0.741 AC: 3573 AN: 4822

European-Finnish (FIN) AF: 0.719 AC: 7571 AN: 10536

Middle Eastern (MID) AF: 0.728 AC: 214 AN: 294

European-Non Finnish (NFE) AF: 0.759 AC: 51494 AN: 67868

Other (OTH) AF: 0.725 AC: 1523 AN: 2102

Alfa AF: 0.693 Hom.: 1463

Asia WGS AF: 0.738 AC: 2567 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.5
DANN	Benign	0.62
PhyloP100		-6.1

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs6586513; hg19: chr1-17216331;