chr11-111879013-C-T
Variant names:
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP7BS2
The NM_138378.3(FDXACB1):c.120G>A(p.Glu40Glu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000456 in 1,613,104 control chromosomes in the GnomAD database, including 6 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 0.00027 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00048 ( 6 hom. )
Consequence
FDXACB1
NM_138378.3 synonymous
NM_138378.3 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.435
Genes affected
FDXACB1 (HGNC:25110): (ferredoxin-fold anticodon binding domain containing 1) This gene encodes a protein which contains a ferredoxin-fold anticodon-binding domain which is contained in a subset of phenylalanyl tRNA synthetases. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -9 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BP7
Synonymous conserved (PhyloP=-0.435 with no splicing effect.
BS2
High Homozygotes in GnomAdExome4 at 6 AR gene
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FDXACB1 | ENST00000260257.9 | c.120G>A | p.Glu40Glu | synonymous_variant | Exon 1 of 5 | 1 | NM_138378.3 | ENSP00000260257.4 | ||
ENSG00000258529 | ENST00000622211.4 | c.120G>A | p.Glu40Glu | synonymous_variant | Exon 1 of 19 | 2 | ENSP00000482396.1 |
Frequencies
GnomAD3 genomes AF: 0.000269 AC: 41AN: 152230Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000842 AC: 206AN: 244792Hom.: 3 AF XY: 0.00111 AC XY: 148AN XY: 133582
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GnomAD4 exome AF: 0.000476 AC: 695AN: 1460756Hom.: 6 Cov.: 32 AF XY: 0.000665 AC XY: 483AN XY: 726634
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GnomAD4 genome AF: 0.000269 AC: 41AN: 152348Hom.: 0 Cov.: 32 AF XY: 0.000336 AC XY: 25AN XY: 74506
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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