rs121434424
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001492.6(GDF1):c.485G>T(p.Gly162Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000665 in 150,336 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 variant affecting the same amino acid position, but resulting in a different missense (i.e. G162D) has been classified as Likely benign.
Frequency
Consequence
NM_001492.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GDF1 | NM_001492.6 | c.485G>T | p.Gly162Val | missense_variant | 8/8 | ENST00000247005.8 | NP_001483.3 | |
CERS1 | NM_021267.5 | c.*754G>T | 3_prime_UTR_variant | 8/8 | ENST00000623882.4 | NP_067090.1 | ||
GDF1 | NM_001387438.1 | c.485G>T | p.Gly162Val | missense_variant | 5/5 | NP_001374367.1 | ||
CERS1 | NM_001387440.1 | c.*1346G>T | 3_prime_UTR_variant | 7/7 | NP_001374369.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GDF1 | ENST00000247005.8 | c.485G>T | p.Gly162Val | missense_variant | 8/8 | 1 | NM_001492.6 | ENSP00000247005 | P1 | |
CERS1 | ENST00000623882.4 | c.*754G>T | 3_prime_UTR_variant | 8/8 | 1 | NM_021267.5 | ENSP00000485308 | P2 |
Frequencies
GnomAD3 genomes AF: 0.00000665 AC: 1AN: 150336Hom.: 0 Cov.: 33
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1238690Hom.: 0 Cov.: 29 AF XY: 0.00 AC XY: 0AN XY: 606732
GnomAD4 genome AF: 0.00000665 AC: 1AN: 150336Hom.: 0 Cov.: 33 AF XY: 0.0000136 AC XY: 1AN XY: 73356
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at