rs1530771

Variant names:

• chr14-80559178-C-A
• rs1530771
• NM_152446.5:c.2880+101G>T

Your query was ambiguous. Multiple possible variants found:

• chr14-80559178-C-A
• chr14-80559178-C-G
• chr14-80559178-C-T

Variant summary

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

The NM_152446.5(CEP128):​c.2880+101G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.539 in 1,051,526 control chromosomes in the GnomAD database, including 154,935 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 0.57 (24601 hom., cov: 31)
  • Exomes 𝑓: 0.53 (130334 hom.)
• Consequence: CEP128 NM_152446.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.10
• Publications: 9 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.701 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.2880+101G>T		intron	N/A	NP_689659.2
	CEP128	NR_157142.2		n.3673+101G>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CEP128	ENST00000555265.6	TSL:5 MANE Select	c.2880+101G>T		intron	N/A	ENSP00000451162.1	Q6ZU80-2
	CEP128	ENST00000281129.7	TSL:1	c.2880+101G>T		intron	N/A	ENSP00000281129.3	Q6ZU80-2
	CEP128	ENST00000947694.1		c.2970+101G>T		intron	N/A	ENSP00000617753.1

Frequencies

GnomAD3 genomes AF: 0.565 AC: 85788 AN: 151766 Hom.: 24550 Cov.: 31

Gnomad AFR AF: 0.646

Gnomad AMI AF: 0.574

Gnomad AMR AF: 0.487

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.720

Gnomad SAS AF: 0.584

Gnomad FIN AF: 0.559

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.527

Gnomad OTH AF: 0.541

GnomAD4 exome AF: 0.534 AC: 480794 AN: 899642 Hom.: 130334 AF XY: 0.537 AC XY: 251885 AN XY: 469362

African (AFR) AF: 0.641 AC: 12958 AN: 20228

American (AMR) AF: 0.432 AC: 13278 AN: 30714

Ashkenazi Jewish (ASJ) AF: 0.462 AC: 9945 AN: 21544

East Asian (EAS) AF: 0.697 AC: 24482 AN: 35146

South Asian (SAS) AF: 0.576 AC: 38122 AN: 66152

European-Finnish (FIN) AF: 0.557 AC: 29097 AN: 52208

Middle Eastern (MID) AF: 0.512 AC: 2379 AN: 4644

European-Non Finnish (NFE) AF: 0.523 AC: 328089 AN: 627588

Other (OTH) AF: 0.542 AC: 22444 AN: 41418

GnomAD4 genome AF: 0.566 AC: 85905 AN: 151884 Hom.: 24601 Cov.: 31 AF XY: 0.564 AC XY: 41886 AN XY: 74224

African (AFR) AF: 0.647 AC: 26787 AN: 41416

American (AMR) AF: 0.486 AC: 7417 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.471 AC: 1630 AN: 3462

East Asian (EAS) AF: 0.720 AC: 3724 AN: 5170

South Asian (SAS) AF: 0.585 AC: 2824 AN: 4826

European-Finnish (FIN) AF: 0.559 AC: 5884 AN: 10520

Middle Eastern (MID) AF: 0.521 AC: 152 AN: 292

European-Non Finnish (NFE) AF: 0.527 AC: 35812 AN: 67938

Other (OTH) AF: 0.549 AC: 1153 AN: 2102

Alfa AF: 0.548 Hom.: 3102

Bravo AF: 0.563

Asia WGS AF: 0.677 AC: 2351 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	10
DANN	Benign	0.49
PhyloP100		1.1
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: rs1530771; hg19: chr14-81025522; COSMIC: COSV55371520;