12-94308506-CA-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_016122.3(CEP83):c.*306del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0585 in 185,194 control chromosomes in the GnomAD database, including 254 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.048 (213 hom., cov: 31)
  • Exomes 𝑓: 0.097 (41 hom.)
• Consequence: CEP83 NM_016122.3 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.0610

Genes affected

CEP83 (HGNC:17966): (centrosomal protein 83) The protein encoded by this gene is a centriolar protein involved in primary cilium assembly. Defects in this gene have been associated with infantile nephronophthisis and intellectual disability. [provided by RefSeq, Oct 2016]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 12-94308506-CA-C is Benign according to our data. Variant chr12-94308506-CA-C is described in ClinVar as [Benign]. Clinvar id is 1282433.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.073 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CEP83	NM_016122.3	c.*306del		3_prime_UTR_variant	17/17	ENST00000397809.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CEP83	ENST00000397809.10	c.*306del		3_prime_UTR_variant	17/17	1	NM_016122.3	P1
CEP83	ENST00000339839.9	c.*306del		3_prime_UTR_variant	16/16	1		P1
CEP83	ENST00000552632.5	c.*30+276del		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.0478 AC: 6922 AN: 144756 Hom.: 212 Cov.: 31

Gnomad AFR AF: 0.0154

Gnomad AMI AF: 0.0168

Gnomad AMR AF: 0.0332

Gnomad ASJ AF: 0.0465

Gnomad EAS AF: 0.000199

Gnomad SAS AF: 0.0227

Gnomad FIN AF: 0.0632

Gnomad MID AF: 0.0545

Gnomad NFE AF: 0.0747

Gnomad OTH AF: 0.0396

GnomAD4 exome AF: 0.0970 AC: 3918 AN: 40382 Hom.: 41 Cov.: 0 AF XY: 0.0956 AC XY: 2049 AN XY: 21438

Gnomad4 AFR exome AF: 0.0552

Gnomad4 AMR exome AF: 0.0781

Gnomad4 ASJ exome AF: 0.0913

Gnomad4 EAS exome AF: 0.0542

Gnomad4 SAS exome AF: 0.0657

Gnomad4 FIN exome AF: 0.0985

Gnomad4 NFE exome AF: 0.109

Gnomad4 OTH exome AF: 0.0960

GnomAD4 genome AF: 0.0478 AC: 6922 AN: 144812 Hom.: 213 Cov.: 31 AF XY: 0.0462 AC XY: 3244 AN XY: 70208

Gnomad4 AFR AF: 0.0154

Gnomad4 AMR AF: 0.0332

Gnomad4 ASJ AF: 0.0465

Gnomad4 EAS AF: 0.000199

Gnomad4 SAS AF: 0.0227

Gnomad4 FIN AF: 0.0632

Gnomad4 NFE AF: 0.0747

Gnomad4 OTH AF: 0.0393

Bravo AF: 0.0427

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Sep 06, 2019

- -

Computational scores

Source: dbNSFP v4.3

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

Publications

LitVar

Other links and lift over

dbSNP: rs568651699; hg19: chr12-94702282;