chr19-1912158-T-G
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 2P and 13B. PM2BP4_StrongBP6_Very_StrongBP7
The NM_138422.4(ADAT3):āc.111T>Gā(p.Pro37=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00028 in 1,569,764 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 (ā ā ).
Frequency
Genomes: š 0.00020 ( 0 hom., cov: 33)
Exomes š: 0.00029 ( 0 hom. )
Consequence
ADAT3
NM_138422.4 synonymous
NM_138422.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.85
Genes affected
ADAT3 (HGNC:25151): (adenosine deaminase tRNA specific 3) This gene encodes a subunit of a tRNA-specific adenosine deaminase. This heterodimeric enzyme converts adenosine to inosine in the tRNA anticodon. A mutation in this gene causes a syndrome characterized by intellectual disability and strabismus. This gene shares its 5' exon with the overlapping gene, secretory carrier membrane protein 4 (Gene ID: 113178). [provided by RefSeq, Jul 2016]
SCAMP4 (HGNC:30385): (secretory carrier membrane protein 4) Secretory carrier membrane proteins (SCAMPs) are widely distributed integral membrane proteins implicated in membrane trafficking. Most SCAMPs (e.g., SCAMP1; MIM 606911) have N-terminal cytoplasmic NPF (arg-pro-phe) repeats, 4 central transmembrane regions, and a short C-terminal cytoplasmic tail. These SCAMPs likely have a role in endocytosis that is mediated by their NPF repeats. Other SCAMPs, such as SCAMP4, lack the NPF repeats and are therefore unlikely to function in endocytosis (summary by Fernandez-Chacon and Sudhof, 2000 [PubMed 11050114]).[supplied by OMIM, Feb 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.93).
BP6
Variant 19-1912158-T-G is Benign according to our data. Variant chr19-1912158-T-G is described in ClinVar as [Likely_benign]. Clinvar id is 726301.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=-1.85 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ADAT3 | NM_138422.4 | c.111T>G | p.Pro37= | synonymous_variant | 2/2 | ENST00000329478.4 | NP_612431.2 | |
SCAMP4 | NM_079834.4 | c.-41-2821T>G | intron_variant | ENST00000316097.13 | NP_524558.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ADAT3 | ENST00000329478.4 | c.111T>G | p.Pro37= | synonymous_variant | 2/2 | 1 | NM_138422.4 | ENSP00000332448 | P1 | |
SCAMP4 | ENST00000316097.13 | c.-41-2821T>G | intron_variant | 1 | NM_079834.4 | ENSP00000316007 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000204 AC: 31AN: 152264Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.000559 AC: 96AN: 171790Hom.: 0 AF XY: 0.000604 AC XY: 57AN XY: 94410
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GnomAD4 exome AF: 0.000289 AC: 409AN: 1417500Hom.: 0 Cov.: 30 AF XY: 0.000310 AC XY: 218AN XY: 702250
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GnomAD4 genome AF: 0.000204 AC: 31AN: 152264Hom.: 0 Cov.: 33 AF XY: 0.000188 AC XY: 14AN XY: 74402
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ClinVar
Significance: Likely benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:3
Likely benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Apr 01, 2023 | ADAT3: BP4, BP7 - |
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 31, 2019 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at