1-243335010-T-C

Position:

• chr1-243335010-T-C

Variant summary

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

The NM_006642.5(SDCCAG8):​c.1221+4318T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.471 in 151,952 control chromosomes in the GnomAD database, including 18,735 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 0.47 (18735 hom., cov: 31)
• Consequence: SDCCAG8 NM_006642.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.29

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=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.724 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SDCCAG8	NM_006642.5	c.1221+4318T>C		intron_variant		ENST00000366541.8	NP_006633.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SDCCAG8	ENST00000366541.8	c.1221+4318T>C		intron_variant		1	NM_006642.5	ENSP00000355499	P1
SDCCAG8	ENST00000435549.1	c.561+4318T>C		intron_variant		1		ENSP00000410200

Frequencies

GnomAD3 genomes AF: 0.471 AC: 71541 AN: 151834 Hom.: 18717 Cov.: 31

Gnomad AFR AF: 0.231

Gnomad AMI AF: 0.455

Gnomad AMR AF: 0.599

Gnomad ASJ AF: 0.518

Gnomad EAS AF: 0.743

Gnomad SAS AF: 0.396

Gnomad FIN AF: 0.619

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.547

Gnomad OTH AF: 0.503

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

GnomAD4 genome AF: 0.471 AC: 71572 AN: 151952 Hom.: 18735 Cov.: 31 AF XY: 0.475 AC XY: 35319 AN XY: 74290

Gnomad4 AFR AF: 0.230

Gnomad4 AMR AF: 0.600

Gnomad4 ASJ AF: 0.518

Gnomad4 EAS AF: 0.743

Gnomad4 SAS AF: 0.395

Gnomad4 FIN AF: 0.619

Gnomad4 NFE AF: 0.547

Gnomad4 OTH AF: 0.507

Alfa AF: 0.530 Hom.: 43272

Bravo AF: 0.460

Asia WGS AF: 0.551 AC: 1917 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	9.1
DANN	Benign	0.64

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: rs2802723; hg19: chr1-243498312;