chr16-15880785-A-T

Variant names:

• chr16-15880785-A-T
• rs72773978
• NM_144600.4:c.227-897T>A

Variant summary

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

The NM_001304499.2(CEP20):​c.299-897T>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_001304499.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.37
• Publications: 9 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001304499.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CEP20	NM_144600.4	MANE Select	c.227-897T>A		intron	N/A	NP_653201.1
	CEP20	NM_001304499.2		c.299-897T>A		intron	N/A	NP_001291428.1
	CEP20	NM_001304502.2		c.299-897T>A		intron	N/A	NP_001291431.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CEP20	ENST00000255759.11	TSL:1 MANE Select	c.227-897T>A		intron	N/A	ENSP00000255759.6
	CEP20	ENST00000929533.1		c.407-897T>A		intron	N/A	ENSP00000599592.1
	CEP20	ENST00000962008.1		c.380-897T>A		intron	N/A	ENSP00000632067.1

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

African (AFR) AF: 0.127 AC: 5247 AN: 41438

American (AMR) AF: 0.0972 AC: 1482 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.0615 AC: 213 AN: 3466

East Asian (EAS) AF: 0.216 AC: 1118 AN: 5166

South Asian (SAS) AF: 0.0488 AC: 235 AN: 4812

European-Finnish (FIN) AF: 0.0242 AC: 257 AN: 10612

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0542 AC: 3686 AN: 67956

Other (OTH) AF: 0.0601 AC: 126 AN: 2098

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.75
DANN	Benign	0.53
PhyloP100		-2.4
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: rs72773978; hg19: chr16-15974642;