NM_144600.4:c.327G>A

Variant names:

• chr16-15873612-C-T
• rs144938295
• NM_144600.4:c.327G>A

Variant summary

Our verdict is Benign. The variant received -11 ACMG points: 0P and 11B. BP4_Strong BP6_Moderate BP7 BS2

The NM_144600.4(CEP20):​c.327G>A​(p.Gly109Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00253 in 1,613,420 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.0026 (0 hom., cov: 33)
  • Exomes 𝑓: 0.0025 (7 hom.)
• Consequence: CEP20 NM_144600.4 synonymous
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.237
• Publications: 1 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 -11 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.51).
• BP6: Variant 16-15873612-C-T is Benign according to our data. Variant chr16-15873612-C-T is described in ClinVar as Likely_benign. ClinVar VariationId is 3387976.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=-0.237 with no splicing effect.
• BS2: High Homozygotes in GnomAdExome4 at 7 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_144600.4. 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
	CEP20	NM_144600.4	MANE Select	c.327G>A	p.Gly109Gly	synonymous	Exon 4 of 5	NP_653201.1	Q96NB1-1
	CEP20	NM_001304499.2		c.399G>A	p.Gly133Gly	synonymous	Exon 5 of 6	NP_001291428.1	I3NI25
	CEP20	NM_001304500.2		c.129G>A	p.Gly43Gly	synonymous	Exon 3 of 4	NP_001291429.1	I3L269

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CEP20	ENST00000255759.11	TSL:1 MANE Select	c.327G>A	p.Gly109Gly	synonymous	Exon 4 of 5	ENSP00000255759.6	Q96NB1-1
	CEP20	ENST00000929533.1		c.507G>A	p.Gly169Gly	synonymous	Exon 6 of 7	ENSP00000599592.1
	CEP20	ENST00000962008.1		c.480G>A	p.Gly160Gly	synonymous	Exon 5 of 6	ENSP00000632067.1

Frequencies

GnomAD3 genomes AF: 0.00257 AC: 391 AN: 152040 Hom.: 0 Cov.: 33

Gnomad AFR AF: 0.000386

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00138

Gnomad ASJ AF: 0.00576

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00378

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00428

Gnomad OTH AF: 0.00144

GnomAD2 exomes AF: 0.00236 AC: 592 AN: 250840 AF XY: 0.00227

Gnomad AFR exome AF: 0.000308

Gnomad AMR exome AF: 0.000551

Gnomad ASJ exome AF: 0.00665

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00421

Gnomad NFE exome AF: 0.00349

Gnomad OTH exome AF: 0.00229

GnomAD4 exome AF: 0.00253 AC: 3692 AN: 1461262 Hom.: 7 Cov.: 30 AF XY: 0.00256 AC XY: 1861 AN XY: 726950

African (AFR) AF: 0.000269 AC: 9 AN: 33474

American (AMR) AF: 0.000627 AC: 28 AN: 44684

Ashkenazi Jewish (ASJ) AF: 0.00659 AC: 172 AN: 26114

East Asian (EAS) AF: 0.0000252 AC: 1 AN: 39678

South Asian (SAS) AF: 0.00 AC: 0 AN: 86184

European-Finnish (FIN) AF: 0.00410 AC: 219 AN: 53372

Middle Eastern (MID) AF: 0.000347 AC: 2 AN: 5764

European-Non Finnish (NFE) AF: 0.00282 AC: 3140 AN: 1111634

Other (OTH) AF: 0.00200 AC: 121 AN: 60358

GnomAD4 genome AF: 0.00257 AC: 391 AN: 152158 Hom.: 0 Cov.: 33 AF XY: 0.00273 AC XY: 203 AN XY: 74372

African (AFR) AF: 0.000385 AC: 16 AN: 41536

American (AMR) AF: 0.00138 AC: 21 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.00576 AC: 20 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5180

South Asian (SAS) AF: 0.00 AC: 0 AN: 4816

European-Finnish (FIN) AF: 0.00378 AC: 40 AN: 10578

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.00428 AC: 291 AN: 68002

Other (OTH) AF: 0.00142 AC: 3 AN: 2110

Alfa AF: 0.00361 Hom.: 0

Bravo AF: 0.00179

Asia WGS AF: 0.000577 AC: 2 AN: 3478

EpiCase AF: 0.00355

EpiControl AF: 0.00302

ClinVar

ClinVar submissions

Significance: Likely benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.13
BayesDel_noAF	Benign	-0.51
CADD	Benign	3.2
DANN	Benign	0.71
PhyloP100		-0.24
Mutation Taster		=99/1	polymorphism

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: rs144938295; hg19: chr16-15967469;