6-13365510-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_018988.4(GFOD1):c.406G>A(p.Glu136Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000049 in 1,612,950 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_018988.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GFOD1 | NM_018988.4 | c.406G>A | p.Glu136Lys | missense_variant | Exon 2 of 2 | ENST00000379287.4 | NP_061861.1 | |
GFOD1 | NM_001242628.2 | c.97G>A | p.Glu33Lys | missense_variant | Exon 2 of 2 | NP_001229557.1 | ||
GFOD1 | NM_001242630.2 | c.97G>A | p.Glu33Lys | missense_variant | Exon 2 of 2 | NP_001229559.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GFOD1 | ENST00000379287.4 | c.406G>A | p.Glu136Lys | missense_variant | Exon 2 of 2 | 1 | NM_018988.4 | ENSP00000368589.3 | ||
GFOD1 | ENST00000379284.1 | c.97G>A | p.Glu33Lys | missense_variant | Exon 2 of 2 | 2 | ENSP00000368586.1 | |||
GFOD1 | ENST00000612338.4 | c.97G>A | p.Glu33Lys | missense_variant | Exon 2 of 2 | 2 | ENSP00000479493.1 |
Frequencies
GnomAD3 genomes AF: 0.0000854 AC: 13AN: 152200Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000760 AC: 19AN: 249916Hom.: 0 AF XY: 0.0000813 AC XY: 11AN XY: 135348
GnomAD4 exome AF: 0.0000452 AC: 66AN: 1460750Hom.: 0 Cov.: 31 AF XY: 0.0000495 AC XY: 36AN XY: 726766
GnomAD4 genome AF: 0.0000854 AC: 13AN: 152200Hom.: 0 Cov.: 32 AF XY: 0.0000672 AC XY: 5AN XY: 74350
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.406G>A (p.E136K) alteration is located in exon 2 (coding exon 2) of the GFOD1 gene. This alteration results from a G to A substitution at nucleotide position 406, causing the glutamic acid (E) at amino acid position 136 to be replaced by a lysine (K). 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