rs2279913

Positions:

• chr17-81194468-A-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_014984.4(CEP131):​c.2120-341T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.486 in 152,030 control chromosomes in the GnomAD database, including 19,032 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 0.49 (19032 hom., cov: 33)
• Consequence: CEP131 NM_014984.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.497

Genes affected

CEP131 (HGNC:29511): (centrosomal protein 131) Enables protein homodimerization activity. Involved in several processes, including intraciliary transport involved in cilium assembly; protein localization to centrosome; and regulation of centrosome duplication. Located in several cellular components, including ciliary transition zone; intercellular bridge; and microtubule organizing center. Colocalizes with centrosome. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.616 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CEP131	NM_014984.4	c.2120-341T>G		intron_variant		ENST00000450824.7	NP_055799.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CEP131	ENST00000450824.7	c.2120-341T>G		intron_variant		1	NM_014984.4	ENSP00000393583	P3

Frequencies

GnomAD3 genomes AF: 0.486 AC: 73828 AN: 151910 Hom.: 19019 Cov.: 33

Gnomad AFR AF: 0.622

Gnomad AMI AF: 0.667

Gnomad AMR AF: 0.355

Gnomad ASJ AF: 0.427

Gnomad EAS AF: 0.131

Gnomad SAS AF: 0.297

Gnomad FIN AF: 0.426

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.483

Gnomad OTH AF: 0.488

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

GnomAD4 genome AF: 0.486 AC: 73869 AN: 152030 Hom.: 19032 Cov.: 33 AF XY: 0.476 AC XY: 35374 AN XY: 74316

Gnomad4 AFR AF: 0.622

Gnomad4 AMR AF: 0.354

Gnomad4 ASJ AF: 0.427

Gnomad4 EAS AF: 0.130

Gnomad4 SAS AF: 0.297

Gnomad4 FIN AF: 0.426

Gnomad4 NFE AF: 0.483

Gnomad4 OTH AF: 0.483

Alfa AF: 0.475 Hom.: 24466

Bravo AF: 0.488

Asia WGS AF: 0.222 AC: 774 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.1
DANN	Benign	0.58

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: rs2279913; hg19: chr17-79168268;