1-45629589-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_021639.5(GPBP1L1):c.1259T>C(p.Met420Thr) variant causes a missense change. The variant allele was found at a frequency of 0.00000374 in 1,605,926 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict 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. M420V) has been classified as Uncertain significance.
Frequency
Consequence
NM_021639.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151814Hom.: 0 Cov.: 28
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251444Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135888
GnomAD4 exome AF: 0.00000275 AC: 4AN: 1454112Hom.: 0 Cov.: 27 AF XY: 0.00000276 AC XY: 2AN XY: 723968
GnomAD4 genome AF: 0.0000132 AC: 2AN: 151814Hom.: 0 Cov.: 28 AF XY: 0.00 AC XY: 0AN XY: 74132
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1259T>C (p.M420T) alteration is located in exon 12 (coding exon 9) of the GPBP1L1 gene. This alteration results from a T to C substitution at nucleotide position 1259, causing the methionine (M) at amino acid position 420 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