chr19-38385791-C-T
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_152657.4(GGN):c.1471G>A(p.Asp491Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00232 in 1,548,736 control chromosomes in the GnomAD database, including 8 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_152657.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GGN | NM_152657.4 | c.1471G>A | p.Asp491Asn | missense_variant | Exon 3 of 4 | ENST00000334928.11 | NP_689870.3 | |
GGN | XM_005258619.5 | c.1471G>A | p.Asp491Asn | missense_variant | Exon 3 of 4 | XP_005258676.1 | ||
GGN | XM_017026451.2 | c.1471G>A | p.Asp491Asn | missense_variant | Exon 2 of 3 | XP_016881940.1 | ||
GGN | XM_011526603.3 | c.1222G>A | p.Asp408Asn | 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.1471G>A | p.Asp491Asn | missense_variant | Exon 3 of 4 | 1 | NM_152657.4 | ENSP00000334940.5 | ||
GGN | ENST00000591809.5 | n.113-291G>A | intron_variant | Intron 2 of 3 | 1 | |||||
GGN | ENST00000585737.1 | n.1222G>A | non_coding_transcript_exon_variant | Exon 3 of 5 | 2 | ENSP00000467295.1 | ||||
ENSG00000267090 | ENST00000585411.1 | n.212+58C>T | intron_variant | Intron 1 of 1 | 3 |
Frequencies
GnomAD3 genomes AF: 0.00193 AC: 293AN: 152068Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00175 AC: 262AN: 149606Hom.: 1 AF XY: 0.00182 AC XY: 151AN XY: 83012
GnomAD4 exome AF: 0.00237 AC: 3306AN: 1396554Hom.: 8 Cov.: 34 AF XY: 0.00226 AC XY: 1559AN XY: 690742
GnomAD4 genome AF: 0.00193 AC: 293AN: 152182Hom.: 0 Cov.: 33 AF XY: 0.00206 AC XY: 153AN XY: 74412
ClinVar
Submissions by phenotype
not provided Benign:2
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GGN-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at