1-89114192-C-T
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_004120.5(GBP2):c.973G>A(p.Ala325Thr) variant causes a missense change. The variant allele was found at a frequency of 0.0000155 in 1,614,118 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_004120.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GBP2 | ENST00000370466.4 | c.973G>A | p.Ala325Thr | missense_variant | Exon 7 of 11 | 1 | NM_004120.5 | ENSP00000359497.3 | ||
GBP2 | ENST00000463660.1 | n.2992G>A | non_coding_transcript_exon_variant | Exon 3 of 5 | 2 | |||||
GBP2 | ENST00000464839.5 | n.973G>A | non_coding_transcript_exon_variant | Exon 10 of 15 | 2 | ENSP00000434282.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152228Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000398 AC: 10AN: 251462Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135900
GnomAD4 exome AF: 0.0000164 AC: 24AN: 1461890Hom.: 0 Cov.: 30 AF XY: 0.0000165 AC XY: 12AN XY: 727246
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152228Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74376
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.973G>A (p.A325T) alteration is located in exon 7 (coding exon 6) of the GBP2 gene. This alteration results from a G to A substitution at nucleotide position 973, causing the alanine (A) at amino acid position 325 to be replaced by a threonine (T). 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