chr1-243484619-C-T

Position:

• chr1-243484619-C-T

Variant summary

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

The NM_006642.5(SDCCAG8):​c.1986-4395C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.262 in 152,128 control chromosomes in the GnomAD database, including 5,881 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 0.26 (5881 hom., cov: 33)
• Consequence: SDCCAG8 NM_006642.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.448

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 = 0.39 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SDCCAG8	NM_006642.5	c.1986-4395C>T		intron_variant		ENST00000366541.8	NP_006633.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SDCCAG8	ENST00000366541.8	c.1986-4395C>T		intron_variant		1	NM_006642.5	ENSP00000355499	P1
SDCCAG8	ENST00000435549.1	c.1089-4395C>T		intron_variant		1		ENSP00000410200

Frequencies

GnomAD3 genomes AF: 0.262 AC: 39803 AN: 152010 Hom.: 5844 Cov.: 33

Gnomad AFR AF: 0.394

Gnomad AMI AF: 0.199

Gnomad AMR AF: 0.236

Gnomad ASJ AF: 0.162

Gnomad EAS AF: 0.396

Gnomad SAS AF: 0.188

Gnomad FIN AF: 0.212

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.197

Gnomad OTH AF: 0.249

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

GnomAD4 genome AF: 0.262 AC: 39909 AN: 152128 Hom.: 5881 Cov.: 33 AF XY: 0.263 AC XY: 19556 AN XY: 74380

Gnomad4 AFR AF: 0.395

Gnomad4 AMR AF: 0.237

Gnomad4 ASJ AF: 0.162

Gnomad4 EAS AF: 0.398

Gnomad4 SAS AF: 0.189

Gnomad4 FIN AF: 0.212

Gnomad4 NFE AF: 0.197

Gnomad4 OTH AF: 0.247

Alfa AF: 0.209 Hom.: 4772

Bravo AF: 0.275

Asia WGS AF: 0.290 AC: 1009 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.2
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: rs2994329; hg19: chr1-243647921;