NM_004864.4:c.566C>T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_004864.4(GDF15):c.566C>T(p.Ala189Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000313 in 1,599,610 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 Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GDF15 | ENST00000252809.3 | c.566C>T | p.Ala189Val | missense_variant | Exon 2 of 2 | 1 | NM_004864.4 | ENSP00000252809.3 | ||
GDF15 | ENST00000595973.3 | c.566C>T | p.Ala189Val | missense_variant | Exon 3 of 3 | 5 | ENSP00000470531.3 | |||
GDF15 | ENST00000597765.2 | c.566C>T | p.Ala189Val | missense_variant | Exon 3 of 3 | 4 | ENSP00000469819.2 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152252Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000140 AC: 3AN: 214910Hom.: 0 AF XY: 0.0000250 AC XY: 3AN XY: 120106
GnomAD4 exome AF: 0.00000138 AC: 2AN: 1447240Hom.: 0 Cov.: 36 AF XY: 0.00000278 AC XY: 2AN XY: 719902
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152370Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74508
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.566C>T (p.A189V) alteration is located in exon 2 (coding exon 2) of the GDF15 gene. This alteration results from a C to T substitution at nucleotide position 566, causing the alanine (A) at amino acid position 189 to be replaced by a valine (V). 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