chr13-23170240-C-T

Variant names:

• chr13-23170240-C-T
• rs9507041
• NM_001378244.1:c.54+9594C>T

Variant summary

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

The NM_001378244.1(SGCG):​c.54+9594C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.122 in 152,152 control chromosomes in the GnomAD database, including 1,185 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 0.12 (1185 hom., cov: 33)
• Consequence: SGCG NM_001378244.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.850
• Publications: 13 publications found

Genes affected

SGCG (HGNC:10809): (sarcoglycan gamma) This gene encodes gamma-sarcoglycan, one of several sarcolemmal transmembrane glycoproteins that interact with dystrophin. The dystrophin-glycoprotein complex (DGC) spans the sarcolemma and is comprised of dystrophin, syntrophin, alpha- and beta-dystroglycans and sarcoglycans. The DGC provides a structural link between the subsarcolemmal cytoskeleton and the extracellular matrix of muscle cells. Defects in the encoded protein can lead to early onset autosomal recessive muscular dystrophy, in particular limb-girdle muscular dystrophy, type 2C (LGMD2C). [provided by RefSeq, Oct 2008]

LINC00362 (HGNC:42682): (long intergenic non-protein coding RNA 362)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.146 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001378244.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SGCG	NM_001378244.1		c.54+9594C>T		intron	N/A	NP_001365173.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00362	ENST00000414345.3	TSL:2	n.338-188G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.122 AC: 18553 AN: 152034 Hom.: 1186 Cov.: 33

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.134

Gnomad AMR AF: 0.135

Gnomad ASJ AF: 0.0841

Gnomad EAS AF: 0.155

Gnomad SAS AF: 0.0987

Gnomad FIN AF: 0.0978

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.115

Gnomad OTH AF: 0.140

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

GnomAD4 genome AF: 0.122 AC: 18562 AN: 152152 Hom.: 1185 Cov.: 33 AF XY: 0.120 AC XY: 8921 AN XY: 74388

African (AFR) AF: 0.136 AC: 5662 AN: 41490

American (AMR) AF: 0.135 AC: 2061 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0841 AC: 292 AN: 3472

East Asian (EAS) AF: 0.155 AC: 802 AN: 5174

South Asian (SAS) AF: 0.0983 AC: 474 AN: 4820

European-Finnish (FIN) AF: 0.0978 AC: 1036 AN: 10592

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.115 AC: 7798 AN: 67998

Other (OTH) AF: 0.139 AC: 293 AN: 2108

Alfa AF: 0.119 Hom.: 5097

Bravo AF: 0.128

Asia WGS AF: 0.116 AC: 405 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.45
DANN	Benign	0.51
PhyloP100		-0.85

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs9507041; hg19: chr13-23744379;