NM_014984.4:c.2120-341T>G

Variant names:

• chr17-81194468-A-C
• rs2279913
• NM_014984.4:c.2120-341T>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 24 publications found

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]

CEP131 Gene-Disease associations (from GenCC):

• male infertility with azoospermia or oligozoospermia due to single gene mutation

  Inheritance: AR Classification: MODERATE Submitted by: King Faisal Specialist Hospital and Research Center

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014984.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CEP131	NM_014984.4	MANE Select	c.2120-341T>G		intron	N/A	NP_055799.2
	CEP131	NM_001319228.2		c.2129-341T>G		intron	N/A	NP_001306157.1
	CEP131	NM_001319229.2		c.2129-341T>G		intron	N/A	NP_001306158.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CEP131	ENST00000450824.7	TSL:1 MANE Select	c.2120-341T>G		intron	N/A	ENSP00000393583.2
	CEP131	ENST00000269392.8	TSL:1	c.2129-341T>G		intron	N/A	ENSP00000269392.4
	CEP131	ENST00000575907.5	TSL:1	c.2129-341T>G		intron	N/A	ENSP00000459733.1

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

African (AFR) AF: 0.622 AC: 25820 AN: 41500

American (AMR) AF: 0.354 AC: 5412 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.427 AC: 1482 AN: 3470

East Asian (EAS) AF: 0.130 AC: 671 AN: 5150

South Asian (SAS) AF: 0.297 AC: 1434 AN: 4824

European-Finnish (FIN) AF: 0.426 AC: 4513 AN: 10590

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.483 AC: 32791 AN: 67902

Other (OTH) AF: 0.483 AC: 1019 AN: 2110

Alfa AF: 0.482 Hom.: 41308

Bravo AF: 0.488

Asia WGS AF: 0.222 AC: 774 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.1
DANN	Benign	0.58
PhyloP100		-0.50
PromoterAI		0.0071	Neutral
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: rs2279913; hg19: chr17-79168268;