1-243381525-C-G

Position:

• chr1-243381525-C-G

Variant summary

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

The NM_006642.5(SDCCAG8):​c.1616+2662C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.777 in 151,880 control chromosomes in the GnomAD database, including 45,922 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 0.78 (45922 hom., cov: 30)
• Consequence: SDCCAG8 NM_006642.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.183

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=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.946 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SDCCAG8	NM_006642.5	c.1616+2662C>G		intron_variant		ENST00000366541.8	NP_006633.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SDCCAG8	ENST00000366541.8	c.1616+2662C>G		intron_variant		1	NM_006642.5	ENSP00000355499	P1
SDCCAG8	ENST00000435549.1	c.956+2662C>G		intron_variant		1		ENSP00000410200
SDCCAG8	ENST00000493334.1	n.583+2662C>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.777 AC: 117888 AN: 151762 Hom.: 45870 Cov.: 30

Gnomad AFR AF: 0.783

Gnomad AMI AF: 0.701

Gnomad AMR AF: 0.848

Gnomad ASJ AF: 0.776

Gnomad EAS AF: 0.968

Gnomad SAS AF: 0.668

Gnomad FIN AF: 0.761

Gnomad MID AF: 0.737

Gnomad NFE AF: 0.753

Gnomad OTH AF: 0.791

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

GnomAD4 genome AF: 0.777 AC: 117999 AN: 151880 Hom.: 45922 Cov.: 30 AF XY: 0.776 AC XY: 57594 AN XY: 74230

Gnomad4 AFR AF: 0.783

Gnomad4 AMR AF: 0.848

Gnomad4 ASJ AF: 0.776

Gnomad4 EAS AF: 0.968

Gnomad4 SAS AF: 0.667

Gnomad4 FIN AF: 0.761

Gnomad4 NFE AF: 0.753

Gnomad4 OTH AF: 0.792

Alfa AF: 0.694 Hom.: 2260

Bravo AF: 0.788

Asia WGS AF: 0.790 AC: 2746 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.45

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: rs1538774; hg19: chr1-243544827;