rs1058587
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_004864.4(GDF15):āc.604C>Gā(p.His202Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.248 in 1,598,956 control chromosomes in the GnomAD database, including 50,515 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 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
NM_004864.4 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.604C>G | p.His202Asp | missense_variant | 2/2 | ENST00000252809.3 | NP_004855.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GDF15 | ENST00000252809.3 | c.604C>G | p.His202Asp | missense_variant | 2/2 | 1 | NM_004864.4 | ENSP00000252809.3 | ||
GDF15 | ENST00000595973.3 | c.604C>G | p.His202Asp | missense_variant | 3/3 | 5 | ENSP00000470531.3 | |||
GDF15 | ENST00000597765.2 | c.604C>G | p.His202Asp | missense_variant | 3/3 | 4 | ENSP00000469819.2 |
Frequencies
GnomAD3 genomes AF: 0.220 AC: 33545AN: 152154Hom.: 3875 Cov.: 34
GnomAD3 exomes AF: 0.243 AC: 53675AN: 220972Hom.: 6693 AF XY: 0.250 AC XY: 30773AN XY: 123056
GnomAD4 exome AF: 0.251 AC: 362783AN: 1446684Hom.: 46642 Cov.: 38 AF XY: 0.253 AC XY: 181921AN XY: 719490
GnomAD4 genome AF: 0.220 AC: 33545AN: 152272Hom.: 3873 Cov.: 34 AF XY: 0.220 AC XY: 16395AN XY: 74462
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at