rs2593068

chr4-55963316-G-Achr4-55963316-G-C

Variant summary

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

The NM_025009.5(CEP135):c.700-958G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.554 in 151,998 control chromosomes in the GnomAD database, including 23,864 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 0.55 (23864 hom., cov: 33)
• Consequence: CEP135 NM_025009.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0800

Genes affected

CEP135 (HGNC:29086): (centrosomal protein 135) This gene encodes a centrosomal protein, which acts as a scaffolding protein during early centriole biogenesis, and is also required for centriole-centriole cohesion during interphase. Mutations in this gene are associated with autosomal recessive primary microcephaly-8. [provided by RefSeq, Jun 2012]

LOC124900705 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.661 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CEP135	NM_025009.5	c.700-958G>A		intron_variant		ENST00000257287.5
LOC124900705	XR_007058124.1	n.197+7457C>T		intron_variant, non_coding_transcript_variant
CEP135	XM_006714055.4	c.700-958G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CEP135	ENST00000257287.5	c.700-958G>A		intron_variant		1	NM_025009.5	P1
CEP135	ENST00000515081.1	n.334-958G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.554 AC: 84140 AN: 151880 Hom.: 23810 Cov.: 33

Gnomad AFR AF: 0.667

Gnomad AMI AF: 0.583

Gnomad AMR AF: 0.612

Gnomad ASJ AF: 0.568

Gnomad EAS AF: 0.423

Gnomad SAS AF: 0.466

Gnomad FIN AF: 0.552

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.487

Gnomad OTH AF: 0.577

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

GnomAD4 genome AF: 0.554 AC: 84243 AN: 151998 Hom.: 23864 Cov.: 33 AF XY: 0.557 AC XY: 41357 AN XY: 74252

Gnomad4 AFR AF: 0.668

Gnomad4 AMR AF: 0.612

Gnomad4 ASJ AF: 0.568

Gnomad4 EAS AF: 0.422

Gnomad4 SAS AF: 0.464

Gnomad4 FIN AF: 0.552

Gnomad4 NFE AF: 0.487

Gnomad4 OTH AF: 0.581

Alfa AF: 0.507 Hom.: 33142

Bravo AF: 0.567

Asia WGS AF: 0.521 AC: 1810 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.67
Dann	Benign	0.59

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: rs2593068; hg19: chr4-56829482;