NM_139167.4:c.40-53246G>A

Variant names:

• chr8-14608172-C-T
• rs7837164
• NM_139167.4:c.40-53246G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_139167.4(SGCZ):​c.40-53246G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.781 in 151,906 control chromosomes in the GnomAD database, including 46,685 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 0.78 (46685 hom., cov: 30)
• Consequence: SGCZ NM_139167.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0390
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.822 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_139167.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SGCZ	NM_139167.4	MANE Select	c.40-53246G>A		intron	N/A	NP_631906.2
	SGCZ	NM_001322879.2		c.40-53246G>A		intron	N/A	NP_001309808.1
	SGCZ	NM_001322880.2		c.40-53246G>A		intron	N/A	NP_001309809.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SGCZ	ENST00000382080.6	TSL:5 MANE Select	c.40-53246G>A		intron	N/A	ENSP00000371512.1

Frequencies

GnomAD3 genomes AF: 0.781 AC: 118519 AN: 151790 Hom.: 46668 Cov.: 30

Gnomad AFR AF: 0.677

Gnomad AMI AF: 0.849

Gnomad AMR AF: 0.805

Gnomad ASJ AF: 0.843

Gnomad EAS AF: 0.797

Gnomad SAS AF: 0.670

Gnomad FIN AF: 0.865

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.828

Gnomad OTH AF: 0.778

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

GnomAD4 genome AF: 0.781 AC: 118579 AN: 151906 Hom.: 46685 Cov.: 30 AF XY: 0.782 AC XY: 58064 AN XY: 74244

African (AFR) AF: 0.677 AC: 28037 AN: 41414

American (AMR) AF: 0.806 AC: 12295 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.843 AC: 2922 AN: 3468

East Asian (EAS) AF: 0.797 AC: 4100 AN: 5144

South Asian (SAS) AF: 0.668 AC: 3212 AN: 4806

European-Finnish (FIN) AF: 0.865 AC: 9119 AN: 10538

Middle Eastern (MID) AF: 0.701 AC: 206 AN: 294

European-Non Finnish (NFE) AF: 0.828 AC: 56289 AN: 67968

Other (OTH) AF: 0.771 AC: 1625 AN: 2108

Alfa AF: 0.805 Hom.: 22174

Bravo AF: 0.775

Asia WGS AF: 0.686 AC: 2388 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.2
DANN	Benign	0.40
PhyloP100		-0.039
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7837164; hg19: chr8-14465681;