chr12-21536516-T-TA
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The NM_021957.4(GYS2):c.*437_*438insT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0235 in 190,982 control chromosomes in the GnomAD database, including 187 homozygotes. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.028 ( 187 hom., cov: 32)
Exomes 𝑓: 0.0041 ( 0 hom. )
Consequence
GYS2
NM_021957.4 3_prime_UTR
NM_021957.4 3_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.412
Genes affected
GYS2 (HGNC:4707): (glycogen synthase 2) The protein encoded by this gene, liver glycogen synthase, catalyzes the rate-limiting step in the synthesis of glycogen - the transfer of a glucose molecule from UDP-glucose to a terminal branch of the glycogen molecule. Mutations in this gene cause glycogen storage disease type 0 (GSD-0) - a rare type of early childhood fasting hypoglycemia with decreased liver glycogen content. [provided by RefSeq, Dec 2009]
SPX (HGNC:28139): (spexin hormone) The protein encoded by this gene is a hormone involved in modulation of cardiovascular and renal function. It has also been shown in rats to cause weight loss. Several transcript variants have been found for this gene. [provided by RefSeq, Feb 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
Variant 12-21536516-T-TA is Benign according to our data. Variant chr12-21536516-T-TA is described in ClinVar as [Likely_benign]. Clinvar id is 307981.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0887 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GYS2 | NM_021957.4 | c.*437_*438insT | 3_prime_UTR_variant | 16/16 | ENST00000261195.3 | ||
LOC124902896 | XR_007063240.1 | n.519-524dup | intron_variant, non_coding_transcript_variant | ||||
GYS2 | XM_006719063.4 | c.*437_*438insT | 3_prime_UTR_variant | 15/15 | |||
GYS2 | XM_024448960.2 | c.*42+395_*42+396insT | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GYS2 | ENST00000261195.3 | c.*437_*438insT | 3_prime_UTR_variant | 16/16 | 1 | NM_021957.4 | P1 | ||
SPX | ENST00000537527.1 | n.472-524dup | intron_variant, non_coding_transcript_variant | 3 | |||||
SPX | ENST00000649016.1 | n.529-524dup | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.0284 AC: 4315AN: 152034Hom.: 186 Cov.: 32
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GnomAD4 exome AF: 0.00412 AC: 160AN: 38830Hom.: 0 Cov.: 0 AF XY: 0.00384 AC XY: 76AN XY: 19812
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GnomAD4 genome AF: 0.0284 AC: 4326AN: 152152Hom.: 187 Cov.: 32 AF XY: 0.0276 AC XY: 2054AN XY: 74386
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Glycogen storage disorder due to hepatic glycogen synthase deficiency Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at