chr19-48993237-G-A

Position:

• chr19-48993237-G-A

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_002103.5(GYS1):​c.-125C>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.078 in 758,922 control chromosomes in the GnomAD database, including 2,757 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.074 (506 hom., cov: 32)
  • Exomes 𝑓: 0.079 (2251 hom.)
• Consequence: GYS1 NM_002103.5 5_prime_UTR_premature_start_codon_gain
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:3
• Conservation: PhyloP100: -0.283

Genes affected

GYS1 (HGNC:4706): (glycogen synthase 1) The protein encoded by this gene catalyzes the addition of glucose monomers to the growing glycogen molecule through the formation of alpha-1,4-glycoside linkages. Mutations in this gene are associated with muscle glycogen storage disease. Alternatively spliced transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Sep 2009]

GYS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BP6: Variant 19-48993237-G-A is Benign according to our data. Variant chr19-48993237-G-A is described in ClinVar as [Benign]. Clinvar id is 329833.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.113 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GYS1	NM_002103.5	c.-125C>T		5_prime_UTR_premature_start_codon_gain_variant	1/16	ENST00000323798.8	NP_002094.2
GYS1	NM_002103.5	c.-125C>T		5_prime_UTR_variant	1/16	ENST00000323798.8	NP_002094.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GYS1	ENST00000323798.8	c.-125C>T		5_prime_UTR_premature_start_codon_gain_variant	1/16	1	NM_002103.5	ENSP00000317904.3
GYS1	ENST00000323798.8	c.-125C>T		5_prime_UTR_variant	1/16	1	NM_002103.5	ENSP00000317904.3

Frequencies

GnomAD3 genomes AF: 0.0745 AC: 11325 AN: 152094 Hom.: 505 Cov.: 32

Gnomad AFR AF: 0.0413

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.0605

Gnomad EAS AF: 0.0761

Gnomad SAS AF: 0.0275

Gnomad FIN AF: 0.136

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0785

Gnomad OTH AF: 0.0804

GnomAD3 exomes AF: 0.0840 AC: 19041 AN: 226674 Hom.: 959 AF XY: 0.0778 AC XY: 9779 AN XY: 125670

Gnomad AFR exome AF: 0.0415

Gnomad AMR exome AF: 0.154

Gnomad ASJ exome AF: 0.0536

Gnomad EAS exome AF: 0.0864

Gnomad SAS exome AF: 0.0284

Gnomad FIN exome AF: 0.139

Gnomad NFE exome AF: 0.0792

Gnomad OTH exome AF: 0.0822

GnomAD4 exome AF: 0.0789 AC: 47860 AN: 606708 Hom.: 2251 Cov.: 5 AF XY: 0.0751 AC XY: 24933 AN XY: 331978

Gnomad4 AFR exome AF: 0.0441

Gnomad4 AMR exome AF: 0.147

Gnomad4 ASJ exome AF: 0.0558

Gnomad4 EAS exome AF: 0.0755

Gnomad4 SAS exome AF: 0.0277

Gnomad4 FIN exome AF: 0.136

Gnomad4 NFE exome AF: 0.0780

Gnomad4 OTH exome AF: 0.0775

GnomAD4 genome AF: 0.0745 AC: 11335 AN: 152214 Hom.: 506 Cov.: 32 AF XY: 0.0765 AC XY: 5695 AN XY: 74430

Gnomad4 AFR AF: 0.0413

Gnomad4 AMR AF: 0.118

Gnomad4 ASJ AF: 0.0605

Gnomad4 EAS AF: 0.0767

Gnomad4 SAS AF: 0.0273

Gnomad4 FIN AF: 0.136

Gnomad4 NFE AF: 0.0785

Gnomad4 OTH AF: 0.0819

Alfa AF: 0.0712 Hom.: 422

Bravo AF: 0.0731

Asia WGS AF: 0.0650 AC: 228 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 16, 2018	This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Glycogen storage disease due to muscle and heart glycogen synthase deficiency Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jan 13, 2018

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	7.1
DANN	Benign	0.88
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

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: rs2287754; hg19: chr19-49496494;