1-45640350-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM1PM2
The NM_021639.5(GPBP1L1):c.604T>C(p.Ser202Pro) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000198 in 1,614,196 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar 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 4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GPBP1L1 | ENST00000355105.8 | c.604T>C | p.Ser202Pro | missense_variant | Exon 8 of 13 | 1 | NM_021639.5 | ENSP00000347224.3 | ||
GPBP1L1 | ENST00000290795.7 | c.604T>C | p.Ser202Pro | missense_variant | Exon 7 of 12 | 5 | ENSP00000290795.3 |
Frequencies
GnomAD3 genomes AF: 0.0000920 AC: 14AN: 152194Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 251480Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135916
GnomAD4 exome AF: 0.0000123 AC: 18AN: 1461884Hom.: 0 Cov.: 31 AF XY: 0.0000110 AC XY: 8AN XY: 727244
GnomAD4 genome AF: 0.0000919 AC: 14AN: 152312Hom.: 0 Cov.: 32 AF XY: 0.000107 AC XY: 8AN XY: 74472
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.604T>C (p.S202P) alteration is located in exon 8 (coding exon 5) of the GPBP1L1 gene. This alteration results from a T to C substitution at nucleotide position 604, causing the serine (S) at amino acid position 202 to be replaced by a proline (P). 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