rs10803140

Positions:

• chr1-243410087-C-G

Variant summary

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

The ENST00000366541.8(SDCCAG8):​c.1617-5615C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.478 in 151,984 control chromosomes in the GnomAD database, including 18,657 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 0.48 (18657 hom., cov: 32)
• Consequence: SDCCAG8 ENST00000366541.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.307

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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.758 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SDCCAG8	NM_006642.5	c.1617-5615C>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.1617-5615C>G		intron_variant		1	NM_006642.5	ENSP00000355499	P1
SDCCAG8	ENST00000435549.1	c.957-16340C>G		intron_variant		1		ENSP00000410200
SDCCAG8	ENST00000493334.1	n.584-5615C>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.478 AC: 72638 AN: 151866 Hom.: 18653 Cov.: 32

Gnomad AFR AF: 0.292

Gnomad AMI AF: 0.445

Gnomad AMR AF: 0.588

Gnomad ASJ AF: 0.519

Gnomad EAS AF: 0.779

Gnomad SAS AF: 0.438

Gnomad FIN AF: 0.526

Gnomad MID AF: 0.599

Gnomad NFE AF: 0.536

Gnomad OTH AF: 0.524

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

GnomAD4 genome AF: 0.478 AC: 72657 AN: 151984 Hom.: 18657 Cov.: 32 AF XY: 0.479 AC XY: 35609 AN XY: 74278

Gnomad4 AFR AF: 0.291

Gnomad4 AMR AF: 0.589

Gnomad4 ASJ AF: 0.519

Gnomad4 EAS AF: 0.779

Gnomad4 SAS AF: 0.437

Gnomad4 FIN AF: 0.526

Gnomad4 NFE AF: 0.536

Gnomad4 OTH AF: 0.527

Alfa AF: 0.480 Hom.: 2240

Bravo AF: 0.474

Asia WGS AF: 0.587 AC: 2040 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.1
DANN	Benign	0.56

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: rs10803140; hg19: chr1-243573389;