19-18388568-A-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_004864.4(GDF15):c.560A>T(p.Gln187Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000691 in 1,446,542 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 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.560A>T | p.Gln187Leu | missense_variant | Exon 2 of 2 | 1 | NM_004864.4 | ENSP00000252809.3 | ||
GDF15 | ENST00000595973.3 | c.560A>T | p.Gln187Leu | missense_variant | Exon 3 of 3 | 5 | ENSP00000470531.3 | |||
GDF15 | ENST00000597765.2 | c.560A>T | p.Gln187Leu | missense_variant | Exon 3 of 3 | 4 | ENSP00000469819.2 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.00000940 AC: 2AN: 212724Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 118920
GnomAD4 exome AF: 6.91e-7 AC: 1AN: 1446542Hom.: 0 Cov.: 36 AF XY: 0.00 AC XY: 0AN XY: 719466
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.560A>T (p.Q187L) alteration is located in exon 2 (coding exon 2) of the GDF15 gene. This alteration results from a A to T substitution at nucleotide position 560, causing the glutamine (Q) at amino acid position 187 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