Variant rs3904682 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The ENST00000366541.8(SDCCAG8):c.-47T>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.499 in 1,563,582 control chromosomes in the GnomAD database, including 204,273 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.42 ( 16060 hom., cov: 33)

Exomes 𝑓: 0.51 ( 188213 hom. )

Consequence

SDCCAG8
ENST00000366541.8 5_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:7

Conservation

PhyloP100: 1.67

Variant links:

Genes affected

SDCCAG8 (HGNC:10671): (SHH signaling and ciliogenesis regulator SDCCAG8) This gene encodes a centrosome associated protein. This protein may be involved in organizing the centrosome during interphase and mitosis. Mutations in this gene are associated with retinal-renal ciliopathy. [provided by RefSeq, Oct 2010]

SDCCAG8 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.53).

BP6

Variant 1-243256127-T-A is Benign according to our data. Variant chr1-243256127-T-A is described in ClinVar as [Benign]. Clinvar id is 260005.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.721 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SDCCAG8	NM_006642.5 linkuse as main transcript	c.-47T>A		5_prime_UTR_variant	1/18	ENST00000366541.8	NP_006633.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SDCCAG8	ENST00000366541.8 linkuse as main transcript	c.-47T>A		5_prime_UTR_variant	1/18	1	NM_006642.5	ENSP00000355499	P1	Q86SQ7-1
SDCCAG8	ENST00000490065.5 linkuse as main transcript	n.94T>A		non_coding_transcript_exon_variant	1/5	4

Frequencies

GnomAD3 genomes

AF:

0.418

AC:

63615

AN:

152026

Hom.:

16038

Cov.:

show subpopulations

Gnomad AFR

AF:

0.126

Gnomad AMI

AF:

0.530

Gnomad AMR

AF:

0.577

Gnomad ASJ

AF:

0.467

Gnomad EAS

AF:

0.740

Gnomad SAS

AF:

0.348

Gnomad FIN

AF:

0.537

Gnomad MID

AF:

0.440

Gnomad NFE

AF:

0.518

Gnomad OTH

AF:

0.468

GnomAD3 exomes

AF:

0.500

AC:

125641

AN:

251130

Hom.:

33948

AF XY:

0.494

AC XY:

67143

AN XY:

135784

show subpopulations

Gnomad AFR exome

AF:

0.116

Gnomad AMR exome

AF:

0.631

Gnomad ASJ exome

AF:

0.466

Gnomad EAS exome

AF:

0.733

Gnomad SAS exome

AF:

0.342

Gnomad FIN exome

AF:

0.545

Gnomad NFE exome

AF:

0.514

Gnomad OTH exome

AF:

0.506

GnomAD4 exome

AF:

0.508

AC:

716456

AN:

1411438

Hom.:

188213

Cov.:

AF XY:

0.502

AC XY:

354204

AN XY:

705442

show subpopulations

Gnomad4 AFR exome

AF:

0.107

Gnomad4 AMR exome

AF:

0.618

Gnomad4 ASJ exome

AF:

0.469

Gnomad4 EAS exome

AF:

0.752

Gnomad4 SAS exome

AF:

0.348

Gnomad4 FIN exome

AF:

0.541

Gnomad4 NFE exome

AF:

0.519

Gnomad4 OTH exome

AF:

0.507

GnomAD4 genome

AF:

0.418

AC:

63648

AN:

152144

Hom.:

16060

Cov.:

AF XY:

0.422

AC XY:

31381

AN XY:

74388

show subpopulations

Gnomad4 AFR

AF:

0.125

Gnomad4 AMR

AF:

0.578

Gnomad4 ASJ

AF:

0.467

Gnomad4 EAS

AF:

0.740

Gnomad4 SAS

AF:

0.349

Gnomad4 FIN

AF:

0.537

Gnomad4 NFE

AF:

0.518

Gnomad4 OTH

AF:

0.472

Alfa

AF:

0.379

Hom.:

1937

Bravo

AF:

0.413

Asia WGS

AF:

0.527

AC:

1832

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:7

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Senior-Loken syndrome 7

Benign:2

Benign, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Jan 13, 2018	This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
Benign, criteria provided, single submitter	clinical testing	Genome-Nilou Lab	Jul 15, 2021	- -

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	May 15, 2021	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Bardet-Biedl syndrome 16

Benign:2

Benign, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Jan 13, 2018	This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
Benign, criteria provided, single submitter	clinical testing	Genome-Nilou Lab	Jul 15, 2021	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.53

CADD

Benign

DANN

Benign

0.76

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over