8-15013412-G-T

Variant names:

• chr8-15013412-G-T
• rs4831667
• NM_139167.4:c.39+224173C>A

Variant summary

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

The NM_139167.4(SGCZ):​c.39+224173C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.325 in 152,028 control chromosomes in the GnomAD database, including 8,558 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 0.32 (8558 hom., cov: 32)
• Consequence: SGCZ NM_139167.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.277

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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.44 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SGCZ	NM_139167.4	c.39+224173C>A		intron_variant	Intron 1 of 7	ENST00000382080.6	NP_631906.2
SGCZ	NM_001322879.2	c.39+224173C>A		intron_variant	Intron 1 of 6		NP_001309808.1
SGCZ	NM_001322880.2	c.39+224173C>A		intron_variant	Intron 1 of 6		NP_001309809.1
SGCZ	NM_001322881.2	c.-90+224173C>A		intron_variant	Intron 1 of 6		NP_001309810.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SGCZ	ENST00000382080.6	c.39+224173C>A		intron_variant	Intron 1 of 7	5	NM_139167.4	ENSP00000371512.1

Frequencies

GnomAD3 genomes AF: 0.325 AC: 49366 AN: 151910 Hom.: 8555 Cov.: 32

Gnomad AFR AF: 0.421

Gnomad AMI AF: 0.256

Gnomad AMR AF: 0.296

Gnomad ASJ AF: 0.374

Gnomad EAS AF: 0.456

Gnomad SAS AF: 0.309

Gnomad FIN AF: 0.254

Gnomad MID AF: 0.439

Gnomad NFE AF: 0.273

Gnomad OTH AF: 0.324

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

GnomAD4 genome AF: 0.325 AC: 49400 AN: 152028 Hom.: 8558 Cov.: 32 AF XY: 0.323 AC XY: 24021 AN XY: 74308

Gnomad4 AFR AF: 0.421

Gnomad4 AMR AF: 0.296

Gnomad4 ASJ AF: 0.374

Gnomad4 EAS AF: 0.455

Gnomad4 SAS AF: 0.310

Gnomad4 FIN AF: 0.254

Gnomad4 NFE AF: 0.273

Gnomad4 OTH AF: 0.327

Alfa AF: 0.293 Hom.: 5363

Bravo AF: 0.336

Asia WGS AF: 0.388 AC: 1345 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.7
DANN	Benign	0.55

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: rs4831667; hg19: chr8-14870921;