chr2-190056112-AT-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2
The NM_005259.3(MSTN):c.*1145del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0113 in 152,206 control chromosomes in the GnomAD database, including 27 homozygotes. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.011 ( 27 hom., cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
MSTN
NM_005259.3 3_prime_UTR
NM_005259.3 3_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.662
Genes affected
MSTN (HGNC:4223): (myostatin) This gene encodes a secreted ligand of the TGF-beta (transforming growth factor-beta) superfamily of proteins. Ligands of this family bind various TGF-beta receptors leading to recruitment and activation of SMAD family transcription factors that regulate gene expression. The encoded preproprotein is proteolytically processed to generate each subunit of the disulfide-linked homodimer. This protein negatively regulates skeletal muscle cell proliferation and differentiation. Mutations in this gene are associated with increased skeletal muscle mass in humans and other mammals. [provided by RefSeq, Jul 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
?
Variant 2-190056112-AT-A is Benign according to our data. Variant chr2-190056112-AT-A is described in ClinVar as [Likely_benign]. Clinvar id is 333220.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0113 (1721/152206) while in subpopulation AFR AF= 0.0389 (1615/41534). AF 95% confidence interval is 0.0373. There are 27 homozygotes in gnomad4. There are 821 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 26 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MSTN | NM_005259.3 | c.*1145del | 3_prime_UTR_variant | 3/3 | ENST00000260950.5 | ||
C2orf88 | XM_047446008.1 | c.-517-23841del | intron_variant | ||||
C2orf88 | XM_047446009.1 | c.-517-23841del | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MSTN | ENST00000260950.5 | c.*1145del | 3_prime_UTR_variant | 3/3 | 1 | NM_005259.3 | P1 | ||
C2orf88 | ENST00000478197.1 | n.220-23110del | intron_variant, non_coding_transcript_variant | 4 | |||||
C2orf88 | ENST00000495546.1 | n.202-23841del | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.0112 AC: 1710AN: 152088Hom.: 26 Cov.: 32
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GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 432Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 260
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Myostatin-related muscle hypertrophy Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at