1-16889836-C-T

Variant names:

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

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000466256.6(CROCC):​n.126-40450C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 44)
• 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 -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).

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>A		upstream_gene	N/A
	LOC105376805	NR_135059.1		n.-170G>A		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>T		intron	N/A
	ENSG00000302843	ENST00000789963.1		n.374-17808C>T		intron	N/A
	ENSG00000238142	ENST00000790083.1		n.95-233G>A		intron	N/A

Frequencies

GnomAD3 genomes Cov.: 44

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

GnomAD4 genome Cov.: 44

Alfa AF: 0.00 Hom.: 1463

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.0
DANN	Benign	0.95
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;