1-243425854-G-T

Position:

• chr1-243425854-G-T

Variant summary

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

The NM_006642.5(SDCCAG8):​c.1854-573G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.503 in 151,920 control chromosomes in the GnomAD database, including 20,680 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 0.50 (20680 hom., cov: 32)
• Consequence: SDCCAG8 NM_006642.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.890

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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.76 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SDCCAG8	NM_006642.5	c.1854-573G>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.1854-573G>T		intron_variant		1	NM_006642.5	ENSP00000355499.3
SDCCAG8	ENST00000435549.1	c.957-573G>T		intron_variant		1		ENSP00000410200.1
SDCCAG8	ENST00000463042.1	n.61-573G>T		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.503 AC: 76389 AN: 151802 Hom.: 20673 Cov.: 32

Gnomad AFR AF: 0.300

Gnomad AMI AF: 0.456

Gnomad AMR AF: 0.618

Gnomad ASJ AF: 0.568

Gnomad EAS AF: 0.780

Gnomad SAS AF: 0.439

Gnomad FIN AF: 0.558

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.572

Gnomad OTH AF: 0.545

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

GnomAD4 genome AF: 0.503 AC: 76409 AN: 151920 Hom.: 20680 Cov.: 32 AF XY: 0.503 AC XY: 37338 AN XY: 74264

Gnomad4 AFR AF: 0.299

Gnomad4 AMR AF: 0.618

Gnomad4 ASJ AF: 0.568

Gnomad4 EAS AF: 0.780

Gnomad4 SAS AF: 0.438

Gnomad4 FIN AF: 0.558

Gnomad4 NFE AF: 0.572

Gnomad4 OTH AF: 0.548

Alfa AF: 0.448 Hom.: 2775

Bravo AF: 0.498

Asia WGS AF: 0.588 AC: 2045 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.27
DANN	Benign	0.42

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: rs10927013; hg19: chr1-243589156;