rs4805834

Positions:

• chr19-32962753-T-A
• chr19-32962753-T-C

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_032816.5(CEP89):​c.147-2695A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: CEP89 NM_032816.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.819

Genes affected

CEP89 (HGNC:25907): (centrosomal protein 89) Involved in non-motile cilium assembly. Acts upstream of or within cilium assembly. Located in several cellular components, including cytosol; microtubule cytoskeleton; and non-motile cilium. Part of ciliary transition fiber. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CEP89	NM_032816.5	c.147-2695A>T		intron_variant		ENST00000305768.10	NP_116205.3
CEP89	XM_005259344.4	c.147-2695A>T		intron_variant			XP_005259401.1
CEP89	XM_017027398.2	c.147-2695A>T		intron_variant			XP_016882887.1
CEP89	XM_047439563.1	c.147-2695A>T		intron_variant			XP_047295519.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CEP89	ENST00000305768.10	c.147-2695A>T		intron_variant		1	NM_032816.5	ENSP00000306105.4
CEP89	ENST00000590597.6	c.147-2695A>T		intron_variant		1		ENSP00000466442.1
CEP89	ENST00000593276.2	c.60-2695A>T		intron_variant		1		ENSP00000467839.1
CEP89	ENST00000586984.6	n.147-2695A>T		intron_variant		1		ENSP00000465141.1

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.15
DANN	Benign	0.20

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: rs4805834; hg19: chr19-33453659;