rs12145833

chr1-243320452-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_006642.5(SDCCAG8):c.1068+3559T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.114 in 152,210 control chromosomes in the GnomAD database, including 1,233 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 0.11 (1233 hom., cov: 32)
• Consequence: SDCCAG8 NM_006642.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.152 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SDCCAG8	NM_006642.5	c.1068+3559T>G		intron_variant		ENST00000366541.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SDCCAG8	ENST00000366541.8	c.1068+3559T>G		intron_variant		1	NM_006642.5	P1
SDCCAG8	ENST00000435549.1	c.408+3559T>G		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.114 AC: 17288 AN: 152092 Hom.: 1232 Cov.: 32

Gnomad AFR AF: 0.0386

Gnomad AMI AF: 0.238

Gnomad AMR AF: 0.132

Gnomad ASJ AF: 0.128

Gnomad EAS AF: 0.0670

Gnomad SAS AF: 0.107

Gnomad FIN AF: 0.132

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.114

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

GnomAD4 genome AF: 0.114 AC: 17289 AN: 152210 Hom.: 1233 Cov.: 32 AF XY: 0.112 AC XY: 8353 AN XY: 74428

Gnomad4 AFR AF: 0.0385

Gnomad4 AMR AF: 0.132

Gnomad4 ASJ AF: 0.128

Gnomad4 EAS AF: 0.0670

Gnomad4 SAS AF: 0.108

Gnomad4 FIN AF: 0.132

Gnomad4 NFE AF: 0.154

Gnomad4 OTH AF: 0.112

Alfa AF: 0.136 Hom.: 329

Bravo AF: 0.111

Asia WGS AF: 0.0660 AC: 229 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.42
Dann	Benign	0.68

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: rs12145833; hg19: chr1-243483754;