19-18386436-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_004864.4(GDF15):c.247G>A(p.Ala83Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000684 in 1,461,076 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 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
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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.247G>A | p.Ala83Thr | missense_variant | Exon 1 of 2 | 1 | NM_004864.4 | ENSP00000252809.3 | ||
GDF15 | ENST00000595973.3 | c.247G>A | p.Ala83Thr | missense_variant | Exon 2 of 3 | 5 | ENSP00000470531.3 | |||
GDF15 | ENST00000597765.2 | c.247G>A | p.Ala83Thr | missense_variant | Exon 2 of 3 | 4 | ENSP00000469819.2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000201 AC: 5AN: 248354Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 134918
GnomAD4 exome AF: 0.00000684 AC: 10AN: 1461076Hom.: 0 Cov.: 33 AF XY: 0.00000688 AC XY: 5AN XY: 726850
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.247G>A (p.A83T) alteration is located in exon 1 (coding exon 1) of the GDF15 gene. This alteration results from a G to A substitution at nucleotide position 247, causing the alanine (A) at amino acid position 83 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