chr16-4799770-G-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_024589.3(ROGDI):c.348C>A(p.Ala116=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000496 in 1,613,162 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. A116A) has been classified as Likely benign.
Frequency
Consequence
NM_024589.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ROGDI | NM_024589.3 | c.348C>A | p.Ala116= | synonymous_variant | 6/11 | ENST00000322048.12 | |
ROGDI | XM_006720947.5 | c.348C>A | p.Ala116= | synonymous_variant | 6/11 | ||
ROGDI | XM_047434636.1 | c.78C>A | p.Ala26= | synonymous_variant | 4/9 | ||
ROGDI | NR_046480.2 | n.355C>A | non_coding_transcript_exon_variant | 5/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ROGDI | ENST00000322048.12 | c.348C>A | p.Ala116= | synonymous_variant | 6/11 | 1 | NM_024589.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152098Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000799 AC: 2AN: 250284Hom.: 0 AF XY: 0.00000739 AC XY: 1AN XY: 135368
GnomAD4 exome AF: 0.00000411 AC: 6AN: 1461064Hom.: 0 Cov.: 30 AF XY: 0.00000413 AC XY: 3AN XY: 726816
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152098Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74262
ClinVar
Submissions by phenotype
Amelocerebrohypohidrotic syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 22, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at