5-57246405-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_022913.4(GPBP1):c.584C>T(p.Pro195Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000139 in 1,613,886 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_022913.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000151 AC: 23AN: 152166Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000103 AC: 26AN: 251274Hom.: 0 AF XY: 0.000132 AC XY: 18AN XY: 135852
GnomAD4 exome AF: 0.000138 AC: 201AN: 1461602Hom.: 0 Cov.: 31 AF XY: 0.000139 AC XY: 101AN XY: 727082
GnomAD4 genome AF: 0.000151 AC: 23AN: 152284Hom.: 0 Cov.: 32 AF XY: 0.000107 AC XY: 8AN XY: 74468
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.605C>T (p.P202L) alteration is located in exon 6 (coding exon 6) of the GPBP1 gene. This alteration results from a C to T substitution at nucleotide position 605, causing the proline (P) at amino acid position 202 to be replaced by a leucine (L). 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