rs2274776
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_145315.5(AFG1L):c.1204-30A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.457 in 1,148,788 control chromosomes in the GnomAD database, including 125,025 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 0.52 ( 21828 hom., cov: 32)
Exomes 𝑓: 0.45 ( 103197 hom. )
Consequence
AFG1L
NM_145315.5 intron
NM_145315.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.19
Genes affected
AFG1L (HGNC:16411): (AFG1 like ATPase) This gene encodes a mitochondrial integral membrane protein that plays a role in mitochondrial protein homeostasis. The protein contains a P-loop motif and a five-domain structure that is conserved in fly, yeast, and bacteria. It functions to mediate the degradation of nuclear-encoded complex IV subunits. Two conserved estrogen receptor binding sites are located within 2.5 kb of this gene. Polymorphisms in this gene have been associated with bipolar disorder. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2016]
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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=-0.88).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.714 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AFG1L | NM_145315.5 | c.1204-30A>G | intron_variant | ENST00000368977.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AFG1L | ENST00000368977.9 | c.1204-30A>G | intron_variant | 1 | NM_145315.5 | P1 | |||
ENST00000659932.1 | n.124-28214T>C | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.520 AC: 79023AN: 151932Hom.: 21802 Cov.: 32
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GnomAD3 exomes AF: 0.442 AC: 102037AN: 230620Hom.: 23826 AF XY: 0.440 AC XY: 54732AN XY: 124492
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GnomAD4 exome AF: 0.448 AC: 446450AN: 996738Hom.: 103197 Cov.: 13 AF XY: 0.446 AC XY: 228895AN XY: 513482
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GnomAD4 genome ? AF: 0.520 AC: 79089AN: 152050Hom.: 21828 Cov.: 32 AF XY: 0.515 AC XY: 38256AN XY: 74306
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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