19-18870253-G-C
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_001492.6(GDF1):āc.55C>Gā(p.Leu19Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000227 in 1,551,400 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001492.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GDF1 | NM_001492.6 | c.55C>G | p.Leu19Val | missense_variant | 7/8 | ENST00000247005.8 | NP_001483.3 | |
CERS1 | NM_021267.5 | c.*324C>G | 3_prime_UTR_variant | 7/8 | ENST00000623882.4 | NP_067090.1 | ||
GDF1 | NM_001387438.1 | c.55C>G | p.Leu19Val | missense_variant | 4/5 | NP_001374367.1 | ||
CERS1 | NM_001387440.1 | c.*324C>G | 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.55C>G | p.Leu19Val | missense_variant | 7/8 | 1 | NM_001492.6 | ENSP00000247005 | P1 | |
CERS1 | ENST00000623882.4 | c.*324C>G | 3_prime_UTR_variant | 7/8 | 1 | NM_021267.5 | ENSP00000485308 | P2 |
Frequencies
GnomAD3 genomes AF: 0.00114 AC: 172AN: 150676Hom.: 3 Cov.: 32
GnomAD3 exomes AF: 0.000297 AC: 44AN: 147950Hom.: 0 AF XY: 0.000210 AC XY: 17AN XY: 80780
GnomAD4 exome AF: 0.000129 AC: 180AN: 1400598Hom.: 1 Cov.: 33 AF XY: 0.000111 AC XY: 77AN XY: 691832
GnomAD4 genome AF: 0.00114 AC: 172AN: 150802Hom.: 3 Cov.: 32 AF XY: 0.00111 AC XY: 82AN XY: 73678
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:3
Likely benign, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, University Medical Center Utrecht | - | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Nov 04, 2016 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Nov 25, 2023 | - - |
Likely benign, no assertion criteria provided | clinical testing | Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ | - | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at