chr19-32963536-C-T

Variant names:

• chr19-32963536-C-T
• rs16967665
• NM_032816.5:c.146+2824G>A

Variant summary

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

The NM_032816.5(CEP89):​c.146+2824G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.138 in 152,134 control chromosomes in the GnomAD database, including 1,470 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 0.14 (1469 hom., cov: 32)
  • Exomes 𝑓: 0.17 (1 hom.)
• Consequence: CEP89 NM_032816.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.873
• Publications: 6 publications found

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]

RPL31P60 (HGNC:36123): (ribosomal protein L31 pseudogene 60)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.273 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032816.5. 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
	CEP89	NM_032816.5	MANE Select	c.146+2824G>A		intron	N/A	NP_116205.3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CEP89	ENST00000305768.10	TSL:1 MANE Select	c.146+2824G>A		intron	N/A	ENSP00000306105.4	Q96ST8-1
	CEP89	ENST00000590597.6	TSL:1	c.146+2824G>A		intron	N/A	ENSP00000466442.1	A0A0C4DGP8
	CEP89	ENST00000593276.2	TSL:1	c.59+2824G>A		intron	N/A	ENSP00000467839.1	K7EQI2

Frequencies

GnomAD3 genomes AF: 0.138 AC: 20913 AN: 151998 Hom.: 1464 Cov.: 32

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.200

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.130

Gnomad EAS AF: 0.285

Gnomad SAS AF: 0.104

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.129

Gnomad OTH AF: 0.139

GnomAD4 exome AF: 0.167 AC: 3 AN: 18 Hom.: 1 Cov.: 0 AF XY: 0.100 AC XY: 1 AN XY: 10

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.167 AC: 3 AN: 18

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.138 AC: 20937 AN: 152116 Hom.: 1469 Cov.: 32 AF XY: 0.137 AC XY: 10212 AN XY: 74352

African (AFR) AF: 0.132 AC: 5486 AN: 41512

American (AMR) AF: 0.152 AC: 2317 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.130 AC: 450 AN: 3468

East Asian (EAS) AF: 0.285 AC: 1473 AN: 5166

South Asian (SAS) AF: 0.103 AC: 498 AN: 4824

European-Finnish (FIN) AF: 0.138 AC: 1452 AN: 10554

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.129 AC: 8754 AN: 68004

Other (OTH) AF: 0.137 AC: 288 AN: 2108

Alfa AF: 0.124 Hom.: 220

Bravo AF: 0.141

Asia WGS AF: 0.153 AC: 535 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.1
DANN	Benign	0.62
PhyloP100		0.87
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: rs16967665; hg19: chr19-33454442;