chr19-18386251-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_004864.4(GDF15):c.62T>C(p.Leu21Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000638 in 1,613,632 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 (★).
Frequency
Consequence
NM_004864.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GDF15 | NM_004864.4 | c.62T>C | p.Leu21Pro | missense_variant | 1/2 | ENST00000252809.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GDF15 | ENST00000252809.3 | c.62T>C | p.Leu21Pro | missense_variant | 1/2 | 1 | NM_004864.4 | P1 | |
GDF15 | ENST00000595973.3 | c.62T>C | p.Leu21Pro | missense_variant | 2/3 | 5 | P1 | ||
GDF15 | ENST00000597765.2 | c.62T>C | p.Leu21Pro | missense_variant | 2/3 | 4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000329 AC: 5AN: 152164Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000319 AC: 8AN: 250778Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135688
GnomAD4 exome AF: 0.0000671 AC: 98AN: 1461468Hom.: 0 Cov.: 46 AF XY: 0.0000550 AC XY: 40AN XY: 727022
GnomAD4 genome ? AF: 0.0000329 AC: 5AN: 152164Hom.: 0 Cov.: 33 AF XY: 0.0000404 AC XY: 3AN XY: 74320
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 22, 2023 | The c.62T>C (p.L21P) alteration is located in exon 1 (coding exon 1) of the GDF15 gene. This alteration results from a T to C substitution at nucleotide position 62, causing the leucine (L) at amino acid position 21 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