19-35536860-C-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_014364.5(GAPDHS):āc.115C>Gā(p.Gln39Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000342 in 1,461,768 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_014364.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GAPDHS | NM_014364.5 | c.115C>G | p.Gln39Glu | missense_variant | 2/11 | ENST00000222286.9 | NP_055179.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GAPDHS | ENST00000222286.9 | c.115C>G | p.Gln39Glu | missense_variant | 2/11 | 1 | NM_014364.5 | ENSP00000222286.3 | ||
GAPDHS | ENST00000585510.1 | c.-90C>G | 5_prime_UTR_variant | 1/6 | 3 | ENSP00000467255.1 | ||||
GAPDHS | ENST00000586334.1 | n.68-1447C>G | intron_variant | 2 | ENSP00000466432.1 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1461768Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 727184
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 26, 2022 | The c.115C>G (p.Q39E) alteration is located in exon 2 (coding exon 2) of the GAPDHS gene. This alteration results from a C to G substitution at nucleotide position 115, causing the glutamine (Q) at amino acid position 39 to be replaced by a glutamic acid (E). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at