1-45634121-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_021639.5(GPBP1L1):c.860G>A(p.Gly287Asp) variant causes a missense change. The variant allele was found at a frequency of 0.0000236 in 1,613,408 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G287S) has been classified as Uncertain significance.
Frequency
Consequence
NM_021639.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GPBP1L1 | ENST00000355105.8 | c.860G>A | p.Gly287Asp | missense_variant | Exon 9 of 13 | 1 | NM_021639.5 | ENSP00000347224.3 | ||
GPBP1L1 | ENST00000290795.7 | c.860G>A | p.Gly287Asp | missense_variant | Exon 8 of 12 | 5 | ENSP00000290795.3 | |||
GPBP1L1 | ENST00000479235.5 | n.1604G>A | non_coding_transcript_exon_variant | Exon 1 of 5 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000112 AC: 17AN: 152188Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000438 AC: 11AN: 251052Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135712
GnomAD4 exome AF: 0.0000144 AC: 21AN: 1461102Hom.: 0 Cov.: 30 AF XY: 0.0000138 AC XY: 10AN XY: 726864
GnomAD4 genome AF: 0.000112 AC: 17AN: 152306Hom.: 0 Cov.: 32 AF XY: 0.000107 AC XY: 8AN XY: 74468
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.860G>A (p.G287D) alteration is located in exon 9 (coding exon 6) of the GPBP1L1 gene. This alteration results from a G to A substitution at nucleotide position 860, causing the glycine (G) at amino acid position 287 to be replaced by an aspartic acid (D). 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