rs72773978

chr16-15880785-A-T

Variant summary

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

The NM_144600.4(CEP20):c.227-897T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0817 in 152,008 control chromosomes in the GnomAD database, including 662 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 0.082 (662 hom., cov: 32)
• Consequence: CEP20 NM_144600.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.37

Genes affected

CEP20 (HGNC:26435): (centrosomal protein 20) Enables identical protein binding activity. Involved in cilium assembly. Located in centriolar satellite and nucleoplasm. [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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.206 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CEP20	NM_144600.4	c.227-897T>A		intron_variant		ENST00000255759.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CEP20	ENST00000255759.11	c.227-897T>A		intron_variant		1	NM_144600.4	P1

Frequencies

GnomAD3 genomes AF: 0.0817 AC: 12408 AN: 151890 Hom.: 662 Cov.: 32

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.0395

Gnomad AMR AF: 0.0969

Gnomad ASJ AF: 0.0615

Gnomad EAS AF: 0.217

Gnomad SAS AF: 0.0494

Gnomad FIN AF: 0.0242

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0542

Gnomad OTH AF: 0.0612

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

GnomAD4 genome AF: 0.0817 AC: 12412 AN: 152008 Hom.: 662 Cov.: 32 AF XY: 0.0823 AC XY: 6115 AN XY: 74320

Gnomad4 AFR AF: 0.127

Gnomad4 AMR AF: 0.0972

Gnomad4 ASJ AF: 0.0615

Gnomad4 EAS AF: 0.216

Gnomad4 SAS AF: 0.0488

Gnomad4 FIN AF: 0.0242

Gnomad4 NFE AF: 0.0542

Gnomad4 OTH AF: 0.0601

Alfa AF: 0.0677 Hom.: 58

Bravo AF: 0.0896

Asia WGS AF: 0.114 AC: 396 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.75
Dann	Benign	0.53

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: rs72773978; hg19: chr16-15974642;