rs149976574
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Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1
The XR_007059016.1(LOC124901120):n.234+20796_234+20806del variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0182 in 152,242 control chromosomes in the GnomAD database, including 313 homozygotes. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.018 ( 313 hom., cov: 33)
Exomes 𝑓: 0.038 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
LOC124901120
XR_007059016.1 intron, non_coding_transcript
XR_007059016.1 intron, non_coding_transcript
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 2.15
Genes affected
SGCD (HGNC:10807): (sarcoglycan delta) The protein encoded by this gene is one of the four known components of the sarcoglycan complex, which is a subcomplex of the dystrophin-glycoprotein complex (DGC). DGC forms a link between the F-actin cytoskeleton and the extracellular matrix. This protein is expressed most abundantly in skeletal and cardiac muscle. Mutations in this gene have been associated with autosomal recessive limb-girdle muscular dystrophy and dilated cardiomyopathy. Alternatively spliced transcript variants encoding distinct isoforms have been observed for this gene. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -16 ACMG points.
BP6
?
Variant 5-156326646-CTGTAATAAGCT-C is Benign according to our data. Variant chr5-156326646-CTGTAATAAGCT-C is described in ClinVar as [Likely_benign]. Clinvar id is 556599.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.323 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LOC124901120 | XR_007059016.1 | n.234+20796_234+20806del | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SGCD | ENST00000517913.5 | c.-43-2884_-43-2874del | intron_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0183 AC: 2791AN: 152126Hom.: 317 Cov.: 33
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0385 AC: 1AN: 26Hom.: 0 AF XY: 0.0625 AC XY: 1AN XY: 16
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Data not reliable, filtered out with message: AS_VQSR
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GnomAD4 genome ? AF: 0.0182 AC: 2775AN: 152242Hom.: 313 Cov.: 33 AF XY: 0.0224 AC XY: 1668AN XY: 74410
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Autosomal recessive limb-girdle muscular dystrophy type 2F Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Feb 08, 2023 | - - |
Autosomal recessive limb-girdle muscular dystrophy type 2F;C1847667:Dilated cardiomyopathy 1L Benign:1
Benign, criteria provided, single submitter | clinical testing | Counsyl | Feb 08, 2018 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | May 26, 2021 | - - |
Dilated cardiomyopathy 1L Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Feb 08, 2023 | - - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at