rs5810000

Variant names:

• chr14-80617101-GA-G
• rs5810000
• NM_152446.5:c.2807-36679delT

Your query was ambiguous. Multiple possible variants found:

• chr14-80617101-GA-G
• chr14-80617101-GA-GAA

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_152446.5(CEP128):​c.2807-36679delT variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.30 (7345 hom., cov: 0)
• Consequence: CEP128 NM_152446.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.166
• Publications: 0 publications found

Genes affected

CEP128 (HGNC:20359): (centrosomal protein 128) Involved in protein localization. Located in centriole and spindle pole. Part of centriolar subdistal appendage. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.485 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_152446.5. 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
	CEP128	NM_152446.5	MANE Select	c.2807-36679delT		intron	N/A	NP_689659.2
	CEP128	NR_157142.2		n.3600-36679delT		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CEP128	ENST00000555265.6	TSL:5 MANE Select	c.2807-36679delT		intron	N/A	ENSP00000451162.1	Q6ZU80-2
	CEP128	ENST00000281129.7	TSL:1	c.2807-36679delT		intron	N/A	ENSP00000281129.3	Q6ZU80-2
	CEP128	ENST00000947694.1		c.2807-36679delT		intron	N/A	ENSP00000617753.1

Frequencies

GnomAD3 genomes AF: 0.303 AC: 45931 AN: 151410 Hom.: 7334 Cov.: 0

Gnomad AFR AF: 0.323

Gnomad AMI AF: 0.400

Gnomad AMR AF: 0.312

Gnomad ASJ AF: 0.396

Gnomad EAS AF: 0.501

Gnomad SAS AF: 0.430

Gnomad FIN AF: 0.172

Gnomad MID AF: 0.379

Gnomad NFE AF: 0.279

Gnomad OTH AF: 0.306

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

GnomAD4 genome AF: 0.303 AC: 45974 AN: 151522 Hom.: 7345 Cov.: 0 AF XY: 0.301 AC XY: 22278 AN XY: 74000

African (AFR) AF: 0.323 AC: 13332 AN: 41324

American (AMR) AF: 0.312 AC: 4750 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.396 AC: 1375 AN: 3468

East Asian (EAS) AF: 0.501 AC: 2571 AN: 5130

South Asian (SAS) AF: 0.430 AC: 2065 AN: 4798

European-Finnish (FIN) AF: 0.172 AC: 1777 AN: 10352

Middle Eastern (MID) AF: 0.387 AC: 113 AN: 292

European-Non Finnish (NFE) AF: 0.279 AC: 18976 AN: 67910

Other (OTH) AF: 0.309 AC: 651 AN: 2108

Alfa AF: 0.279 Hom.: 739

Bravo AF: 0.311

Asia WGS AF: 0.460 AC: 1600 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.17
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: rs5810000; hg19: chr14-81083445;