19-38385623-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_152657.4(GGN):c.1639G>A(p.Gly547Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00177 in 1,614,118 control chromosomes in the GnomAD database, including 39 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G547D) has been classified as Uncertain significance.
Frequency
Consequence
NM_152657.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GGN | NM_152657.4 | c.1639G>A | p.Gly547Ser | missense_variant | Exon 3 of 4 | ENST00000334928.11 | NP_689870.3 | |
GGN | XM_005258619.5 | c.1639G>A | p.Gly547Ser | missense_variant | Exon 3 of 4 | XP_005258676.1 | ||
GGN | XM_017026451.2 | c.1639G>A | p.Gly547Ser | missense_variant | Exon 2 of 3 | XP_016881940.1 | ||
GGN | XM_011526603.3 | c.1390G>A | p.Gly464Ser | missense_variant | Exon 3 of 4 | XP_011524905.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GGN | ENST00000334928.11 | c.1639G>A | p.Gly547Ser | missense_variant | Exon 3 of 4 | 1 | NM_152657.4 | ENSP00000334940.5 | ||
GGN | ENST00000591809.5 | n.113-123G>A | intron_variant | Intron 2 of 3 | 1 | |||||
ENSG00000267090 | ENST00000585411.1 | n.102C>T | non_coding_transcript_exon_variant | Exon 1 of 2 | 3 | |||||
GGN | ENST00000585737.1 | n.1366+24G>A | intron_variant | Intron 3 of 4 | 2 | ENSP00000467295.1 |
Frequencies
GnomAD3 genomes AF: 0.00862 AC: 1312AN: 152248Hom.: 21 Cov.: 33
GnomAD3 exomes AF: 0.00247 AC: 618AN: 250350Hom.: 8 AF XY: 0.00185 AC XY: 251AN XY: 135580
GnomAD4 exome AF: 0.00105 AC: 1540AN: 1461752Hom.: 18 Cov.: 34 AF XY: 0.000912 AC XY: 663AN XY: 727198
GnomAD4 genome AF: 0.00862 AC: 1313AN: 152366Hom.: 21 Cov.: 33 AF XY: 0.00874 AC XY: 651AN XY: 74512
ClinVar
Submissions by phenotype
not provided Benign:2
- -
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at