Variant 1-243344378-C-CA details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The NM_006642.5(SDCCAG8):c.1473+48dup variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.27 in 1,194,606 control chromosomes in the GnomAD database, including 47,252 homozygotes. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.26 ( 5333 hom., cov: 24)

Exomes 𝑓: 0.27 ( 41919 hom. )

Consequence

SDCCAG8
NM_006642.5 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -0.0960

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP6

Variant 1-243344378-C-CA is Benign according to our data. Variant chr1-243344378-C-CA is described in ClinVar as [Benign]. Clinvar id is 260008.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.338 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.1473+48dup		intron_variant		ENST00000366541.8	NP_006633.1

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	Appris	UniProt
SDCCAG8	ENST00000366541.8 linkuse as main transcript	c.1473+48dup	intron_variant	1	NM_006642.5	ENSP00000355499	P1	Q86SQ7-1
SDCCAG8	ENST00000435549.1 linkuse as main transcript	c.813+48dup	intron_variant	1		ENSP00000410200
SDCCAG8	ENST00000493334.1 linkuse as main transcript	n.440+48dup	intron_variant, non_coding_transcript_variant	5

Frequencies

GnomAD3 genomes

AF:

0.262

AC:

39751

AN:

151938

Hom.:

5330

Cov.:

show subpopulations

Gnomad AFR

AF:

0.269

Gnomad AMI

AF:

0.317

Gnomad AMR

AF:

0.197

Gnomad ASJ

AF:

0.260

Gnomad EAS

AF:

0.0340

Gnomad SAS

AF:

0.352

Gnomad FIN

AF:

0.246

Gnomad MID

AF:

0.344

Gnomad NFE

AF:

0.284

Gnomad OTH

AF:

0.261

GnomAD3 exomes

AF:

0.253

AC:

63042

AN:

248724

Hom.:

9000

AF XY:

0.267

AC XY:

35833

AN XY:

134444

show subpopulations

Gnomad AFR exome

AF:

0.276

Gnomad AMR exome

AF:

0.132

Gnomad ASJ exome

AF:

0.269

Gnomad EAS exome

AF:

0.0388

Gnomad SAS exome

AF:

0.368

Gnomad FIN exome

AF:

0.253

Gnomad NFE exome

AF:

0.289

Gnomad OTH exome

AF:

0.272

GnomAD4 exome

AF:

0.271

AC:

282697

AN:

1042550

Hom.:

41919

Cov.:

AF XY:

0.277

AC XY:

149136

AN XY:

537912

show subpopulations

Gnomad4 AFR exome

AF:

0.273

Gnomad4 AMR exome

AF:

0.139

Gnomad4 ASJ exome

AF:

0.256

Gnomad4 EAS exome

AF:

0.0247

Gnomad4 SAS exome

AF:

0.364

Gnomad4 FIN exome

AF:

0.258

Gnomad4 NFE exome

AF:

0.283

Gnomad4 OTH exome

AF:

0.272

GnomAD4 genome

AF:

0.262

AC:

39772

AN:

152056

Hom.:

5333

Cov.:

AF XY:

0.261

AC XY:

19377

AN XY:

74338

show subpopulations

Gnomad4 AFR

AF:

0.269

Gnomad4 AMR

AF:

0.196

Gnomad4 ASJ

AF:

0.260

Gnomad4 EAS

AF:

0.0339

Gnomad4 SAS

AF:

0.352

Gnomad4 FIN

AF:

0.246

Gnomad4 NFE

AF:

0.284

Gnomad4 OTH

AF:

0.260

Alfa

AF:

0.282

Hom.:

1302

Bravo

AF:

0.255

Asia WGS

AF:

0.227

AC:

791

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

Senior-Loken syndrome 7

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 15, 2021

- -

Bardet-Biedl syndrome 16

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 15, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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