chr19-18386331-T-A
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000252809.3(GDF15):c.142T>A(p.Ser48Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.24 in 1,613,728 control chromosomes in the GnomAD database, including 48,582 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
ENST00000252809.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GDF15 | NM_004864.4 | c.142T>A | p.Ser48Thr | missense_variant | 1/2 | ENST00000252809.3 | NP_004855.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GDF15 | ENST00000252809.3 | c.142T>A | p.Ser48Thr | missense_variant | 1/2 | 1 | NM_004864.4 | ENSP00000252809 | P1 | |
GDF15 | ENST00000595973.3 | c.142T>A | p.Ser48Thr | missense_variant | 2/3 | 5 | ENSP00000470531 | P1 | ||
GDF15 | ENST00000597765.2 | c.142T>A | p.Ser48Thr | missense_variant | 2/3 | 4 | ENSP00000469819 | P1 |
Frequencies
GnomAD3 genomes AF: 0.241 AC: 36599AN: 151936Hom.: 4727 Cov.: 32
GnomAD3 exomes AF: 0.273 AC: 68427AN: 250812Hom.: 10237 AF XY: 0.265 AC XY: 35959AN XY: 135656
GnomAD4 exome AF: 0.240 AC: 350953AN: 1461674Hom.: 43849 Cov.: 37 AF XY: 0.238 AC XY: 173029AN XY: 727146
GnomAD4 genome AF: 0.241 AC: 36639AN: 152054Hom.: 4733 Cov.: 32 AF XY: 0.246 AC XY: 18285AN XY: 74306
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at