8-15220912-T-G

Variant summary

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

The NM_139167.4(SGCZ):c.39+16673A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.885 in 152,066 control chromosomes in the GnomAD database, including 59,738 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 0.89 (59738 hom., cov: 30)
• Consequence: SGCZ NM_139167.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.799

Genes affected

SGCZ (HGNC:14075): (sarcoglycan zeta) The zeta-sarcoglycan gene measures over 465 kb and localizes to 8p22. This protein is part of the sarcoglycan complex, a group of 6 proteins. The sarcoglycans are all N-glycosylated transmembrane proteins with a short intra-cellular domain, a single transmembrane region and a large extra-cellular domain containing a carboxyl-terminal cluster with several conserved cysteine residues. The sarcoglycan complex is part of the dystrophin-associated glycoprotein complex (DGC), which bridges the inner cytoskeleton and the extra-cellular matrix. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.9 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SGCZ	NM_139167.4	c.39+16673A>C		intron_variant		ENST00000382080.6
SGCZ	NM_001322879.2	c.39+16673A>C		intron_variant
SGCZ	NM_001322880.2	c.39+16673A>C		intron_variant
SGCZ	NM_001322881.2	c.-90+16673A>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SGCZ	ENST00000382080.6	c.39+16673A>C		intron_variant		5	NM_139167.4	P1

Frequencies

GnomAD3 genomes AF: 0.885 AC: 134541 AN: 151950 Hom.: 59700 Cov.: 30

Gnomad AFR AF: 0.852

Gnomad AMI AF: 0.978

Gnomad AMR AF: 0.856

Gnomad ASJ AF: 0.881

Gnomad EAS AF: 0.794

Gnomad SAS AF: 0.894

Gnomad FIN AF: 0.957

Gnomad MID AF: 0.886

Gnomad NFE AF: 0.906

Gnomad OTH AF: 0.893

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

GnomAD4 genome AF: 0.885 AC: 134638 AN: 152066 Hom.: 59738 Cov.: 30 AF XY: 0.888 AC XY: 66054 AN XY: 74344

Gnomad4 AFR AF: 0.851

Gnomad4 AMR AF: 0.856

Gnomad4 ASJ AF: 0.881

Gnomad4 EAS AF: 0.794

Gnomad4 SAS AF: 0.894

Gnomad4 FIN AF: 0.957

Gnomad4 NFE AF: 0.906

Gnomad4 OTH AF: 0.894

Alfa AF: 0.900 Hom.: 2976

Bravo AF: 0.874

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.87
Dann	Benign	0.38

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: rs268346; hg19: chr8-15078421;