1-16889836-C-G

Variant names:

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

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000466256.6(CROCC):​n.126-40450C>G 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

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]

ENSG00000238142 (HGNC:):

TRN-GTT4-1 (HGNC:33197):

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRN-GTT4-1	unassigned_transcript_43	c.*86C>G		downstream_gene_variant
LOC105376805	NR_135058.1	n.-170G>C		upstream_gene_variant
LOC105376805	NR_135059.1	n.-170G>C		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CROCC	ENST00000466256.6	n.126-40450C>G		intron_variant	Intron 1 of 8	5
ENSG00000238142	ENST00000457075.1	n.-187G>C		upstream_gene_variant		1
ENSG00000238142	ENST00000416869.2	n.-143G>C		upstream_gene_variant		2

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

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.7
DANN	Benign	0.12

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6586513; hg19: chr1-17216331;