chr19-18388357-G-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_004864.4(GDF15):c.349G>A(p.Ala117Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000482 in 1,611,574 control chromosomes in the GnomAD database, including 8 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A117D) has been classified as Benign.
Frequency
Consequence
NM_004864.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GDF15 | NM_004864.4 | c.349G>A | p.Ala117Thr | missense_variant | 2/2 | ENST00000252809.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GDF15 | ENST00000252809.3 | c.349G>A | p.Ala117Thr | missense_variant | 2/2 | 1 | NM_004864.4 | P1 | |
GDF15 | ENST00000595973.3 | c.349G>A | p.Ala117Thr | missense_variant | 3/3 | 5 | P1 | ||
GDF15 | ENST00000597765.2 | c.349G>A | p.Ala117Thr | missense_variant | 3/3 | 4 | P1 | ||
GDF15 | ENST00000594925.1 | n.167G>A | non_coding_transcript_exon_variant | 2/2 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00250 AC: 381AN: 152194Hom.: 3 Cov.: 33
GnomAD3 exomes AF: 0.000756 AC: 183AN: 242058Hom.: 3 AF XY: 0.000564 AC XY: 75AN XY: 133060
GnomAD4 exome AF: 0.000270 AC: 394AN: 1459262Hom.: 5 Cov.: 34 AF XY: 0.000241 AC XY: 175AN XY: 725976
GnomAD4 genome ? AF: 0.00251 AC: 382AN: 152312Hom.: 3 Cov.: 33 AF XY: 0.00238 AC XY: 177AN XY: 74472
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Aug 16, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at