rs6586513

chr1-16889836-C-Achr1-16889836-C-Gchr1-16889836-C-T

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000466256.6(CROCC):n.126-40450C>A variant causes a intron, non coding transcript 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, non_coding_transcript
• 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]

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CROCC	ENST00000466256.6	n.126-40450C>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.00 AC: 107595 AN: 151136 Hom.: 33688 Cov.: 44 FAILED QC

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

Gnomad4 AFR AF: 0.598

Gnomad4 AMR AF: 0.725

Gnomad4 ASJ AF: 0.770

Gnomad4 EAS AF: 0.852

Gnomad4 SAS AF: 0.741

Gnomad4 FIN AF: 0.719

Gnomad4 NFE AF: 0.759

Gnomad4 OTH AF: 0.725

Alfa AF: 0.693 Hom.: 1463

Asia WGS AF: 0.738 AC: 2567 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	1.5
Dann	Benign	0.62

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;