chr21-25764304-G-A
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2
The NM_002040.4(GABPA):c.897G>A(p.Ala299=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00169 in 1,612,374 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0015 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0017 ( 6 hom. )
Consequence
GABPA
NM_002040.4 synonymous
NM_002040.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.227
Genes affected
GABPA (HGNC:4071): (GA binding protein transcription factor subunit alpha) This gene encodes one of three GA-binding protein transcription factor subunits which functions as a DNA-binding subunit. Since this subunit shares identity with a subunit encoding the nuclear respiratory factor 2 gene, it is likely involved in activation of cytochrome oxidase expression and nuclear control of mitochondrial function. This subunit also shares identity with a subunit constituting the transcription factor E4TF1, responsible for expression of the adenovirus E4 gene. Because of its chromosomal localization and ability to form heterodimers with other polypeptides, this gene may play a role in the Down Syndrome phenotype. Two transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Oct 2010]
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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=-0.43).
BP6
?
Variant 21-25764304-G-A is Benign according to our data. Variant chr21-25764304-G-A is described in ClinVar as [Benign]. Clinvar id is 733491.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-0.227 with no splicing effect.
BS2
?
High AC in GnomAd at 225 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GABPA | NM_002040.4 | c.897G>A | p.Ala299= | synonymous_variant | 8/10 | ENST00000400075.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GABPA | ENST00000400075.4 | c.897G>A | p.Ala299= | synonymous_variant | 8/10 | 1 | NM_002040.4 | P1 | |
GABPA | ENST00000354828.7 | c.897G>A | p.Ala299= | synonymous_variant | 8/10 | 1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00148 AC: 225AN: 152034Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.00158 AC: 395AN: 250276Hom.: 0 AF XY: 0.00159 AC XY: 215AN XY: 135444
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GnomAD4 exome AF: 0.00171 AC: 2495AN: 1460222Hom.: 6 Cov.: 32 AF XY: 0.00172 AC XY: 1250AN XY: 726412
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GnomAD4 genome ? AF: 0.00148 AC: 225AN: 152152Hom.: 0 Cov.: 32 AF XY: 0.00141 AC XY: 105AN XY: 74390
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 20, 2017 | - - |
Computational scores
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Benign
Cadd
Benign
Dann
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at