rs509556
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001104.4(ACTN3):c.1277-345A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.586 in 247,114 control chromosomes in the GnomAD database, including 44,593 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 0.61 ( 30027 hom., cov: 32)
Exomes 𝑓: 0.55 ( 14566 hom. )
Consequence
ACTN3
NM_001104.4 intron
NM_001104.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.06
Genes affected
ACTN3 (HGNC:165): (actinin alpha 3) This gene encodes a member of the alpha-actin binding protein gene family. The encoded protein is primarily expressed in skeletal muscle and functions as a structural component of sarcomeric Z line. This protein is involved in crosslinking actin containing thin filaments. An allelic polymorphism in this gene results in both coding and non-coding variants; the reference genome represents the coding allele. The non-functional allele of this gene is associated with elite athlete status. [provided by RefSeq, Feb 2014]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-1.0).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.825 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ACTN3 | NM_001104.4 | c.1277-345A>G | intron_variant | ENST00000513398.2 | |||
ACTN3 | NM_001258371.3 | c.1406-345A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ACTN3 | ENST00000513398.2 | c.1277-345A>G | intron_variant | 1 | NM_001104.4 | P1 | |||
ENST00000504911.1 | n.555T>C | non_coding_transcript_exon_variant | 2/2 | 3 | |||||
ACTN3 | ENST00000502692.5 | c.1406-345A>G | intron_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.611 AC: 92891AN: 151974Hom.: 29968 Cov.: 32
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GnomAD4 exome AF: 0.546 AC: 51836AN: 95022Hom.: 14566 Cov.: 0 AF XY: 0.541 AC XY: 25905AN XY: 47922
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GnomAD4 genome ? AF: 0.611 AC: 92999AN: 152092Hom.: 30027 Cov.: 32 AF XY: 0.607 AC XY: 45134AN XY: 74348
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at