rs11107531

Variant names:

• chr12-94407545-C-T
• rs11107531
• NM_016122.3:c.324+4152G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_016122.3(CEP83):​c.324+4152G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.256 in 152,098 control chromosomes in the GnomAD database, including 5,081 homozygotes. 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 0.26 (5081 hom., cov: 32)
• Consequence: CEP83 NM_016122.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.20
• Publications: 1 publications found

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]

CEP83 Gene-Disease associations (from GenCC):

• nephronophthisis 18

  Inheritance: AR Classification: DEFINITIVE, STRONG, MODERATE Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics, Genomics England PanelApp, G2P
• nephronophthisis 2

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.29 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CEP83	NM_016122.3	c.324+4152G>A		intron_variant	Intron 4 of 16	ENST00000397809.10	NP_057206.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CEP83	ENST00000397809.10	c.324+4152G>A		intron_variant	Intron 4 of 16	1	NM_016122.3	ENSP00000380911.4

Frequencies

GnomAD3 genomes AF: 0.255 AC: 38824 AN: 151980 Hom.: 5073 Cov.: 32

Gnomad AFR AF: 0.289

Gnomad AMI AF: 0.275

Gnomad AMR AF: 0.297

Gnomad ASJ AF: 0.199

Gnomad EAS AF: 0.173

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.302

Gnomad MID AF: 0.274

Gnomad NFE AF: 0.237

Gnomad OTH AF: 0.256

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

GnomAD4 genome AF: 0.256 AC: 38871 AN: 152098 Hom.: 5081 Cov.: 32 AF XY: 0.257 AC XY: 19086 AN XY: 74352

African (AFR) AF: 0.289 AC: 11997 AN: 41470

American (AMR) AF: 0.297 AC: 4539 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.199 AC: 689 AN: 3470

East Asian (EAS) AF: 0.173 AC: 893 AN: 5172

South Asian (SAS) AF: 0.123 AC: 592 AN: 4826

European-Finnish (FIN) AF: 0.302 AC: 3190 AN: 10570

Middle Eastern (MID) AF: 0.284 AC: 83 AN: 292

European-Non Finnish (NFE) AF: 0.237 AC: 16100 AN: 67988

Other (OTH) AF: 0.255 AC: 539 AN: 2112

Alfa AF: 0.245 Hom.: 7875

Bravo AF: 0.262

Asia WGS AF: 0.154 AC: 535 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.011
DANN	Benign	0.42
PhyloP100		-3.2
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs11107531; hg19: chr12-94801321;