chr21-25764303-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 1P and 6B. PP2BP4_ModerateBS2
The NM_002040.4(GABPA):c.896C>T(p.Ala299Val) variant causes a missense change. The variant allele was found at a frequency of 0.0000285 in 1,612,142 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. A299A) has been classified as Benign.
Frequency
Consequence
NM_002040.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GABPA | NM_002040.4 | c.896C>T | p.Ala299Val | missense_variant | 8/10 | ENST00000400075.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GABPA | ENST00000400075.4 | c.896C>T | p.Ala299Val | missense_variant | 8/10 | 1 | NM_002040.4 | P1 | |
GABPA | ENST00000354828.7 | c.896C>T | p.Ala299Val | missense_variant | 8/10 | 1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000132 AC: 2AN: 151966Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000240 AC: 6AN: 250326Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135472
GnomAD4 exome AF: 0.0000301 AC: 44AN: 1460176Hom.: 0 Cov.: 32 AF XY: 0.0000248 AC XY: 18AN XY: 726374
GnomAD4 genome ? AF: 0.0000132 AC: 2AN: 151966Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74230
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 27, 2023 | The c.896C>T (p.A299V) alteration is located in exon 8 (coding exon 7) of the GABPA gene. This alteration results from a C to T substitution at nucleotide position 896, causing the alanine (A) at amino acid position 299 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at