17-6589554-AAAG-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_014804.3(KIAA0753):c.2786+222_2786+224del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.117 in 151,548 control chromosomes in the GnomAD database, including 1,621 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.12 (1621 hom., cov: 31)
• Consequence: KIAA0753 NM_014804.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.0930

Genes affected

KIAA0753 (HGNC:29110): (KIAA0753) This gene encodes a subunit of a protein complex that regulates ciliogenesis and cilia maintenance. The encoded protein has also been shown to regulate centriolar duplication. Mutations in this gene cause an orofaciodigital syndrome and a form of Joubert syndrome in human patients. [provided by RefSeq, May 2017]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 17-6589554-AAAG-A is Benign according to our data. Variant chr17-6589554-AAAG-A is described in ClinVar as [Benign]. Clinvar id is 1181856.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.343 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KIAA0753	NM_014804.3	c.2786+222_2786+224del		intron_variant		ENST00000361413.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KIAA0753	ENST00000361413.8	c.2786+222_2786+224del		intron_variant		1	NM_014804.3	P1

Frequencies

GnomAD3 genomes AF: 0.117 AC: 17694 AN: 151430 Hom.: 1610 Cov.: 31

Gnomad AFR AF: 0.188

Gnomad AMI AF: 0.215

Gnomad AMR AF: 0.173

Gnomad ASJ AF: 0.0763

Gnomad EAS AF: 0.357

Gnomad SAS AF: 0.181

Gnomad FIN AF: 0.0309

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.0533

Gnomad OTH AF: 0.106

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

GnomAD4 genome AF: 0.117 AC: 17719 AN: 151548 Hom.: 1621 Cov.: 31 AF XY: 0.120 AC XY: 8884 AN XY: 74062

Gnomad4 AFR AF: 0.187

Gnomad4 AMR AF: 0.173

Gnomad4 ASJ AF: 0.0763

Gnomad4 EAS AF: 0.357

Gnomad4 SAS AF: 0.180

Gnomad4 FIN AF: 0.0309

Gnomad4 NFE AF: 0.0533

Gnomad4 OTH AF: 0.115

Alfa AF: 0.0836 Hom.: 95

Bravo AF: 0.131

Asia WGS AF: 0.230 AC: 751 AN: 3270

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 13, 2021

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Computational scores

Source: dbNSFP v4.3

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: rs71157203; hg19: chr17-6492874;