19-1912164-G-A

Variant summary

Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2

The NM_138422.4(ADAT3):​c.117G>A​(p.Pro39=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00522 in 1,572,282 control chromosomes in the GnomAD database, including 23 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0034 ( 2 hom., cov: 33)
Exomes 𝑓: 0.0054 ( 21 hom. )

Consequence

ADAT3
NM_138422.4 synonymous

Scores

2

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -4.94
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -17 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BP6
Variant 19-1912164-G-A is Benign according to our data. Variant chr19-1912164-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 718244.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=-4.94 with no splicing effect.
BS2
High Homozygotes in GnomAd4 at 2 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
ADAT3NM_138422.4 linkuse as main transcriptc.117G>A p.Pro39= synonymous_variant 2/2 ENST00000329478.4 NP_612431.2
SCAMP4NM_079834.4 linkuse as main transcriptc.-41-2815G>A intron_variant ENST00000316097.13 NP_524558.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ADAT3ENST00000329478.4 linkuse as main transcriptc.117G>A p.Pro39= synonymous_variant 2/21 NM_138422.4 ENSP00000332448 P1
SCAMP4ENST00000316097.13 linkuse as main transcriptc.-41-2815G>A intron_variant 1 NM_079834.4 ENSP00000316007 P1Q969E2-1

Frequencies

GnomAD3 genomes
AF:
0.00339
AC:
516
AN:
152264
Hom.:
2
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.000916
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00216
Gnomad ASJ
AF:
0.00259
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00207
Gnomad FIN
AF:
0.00150
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00595
Gnomad OTH
AF:
0.00239
GnomAD3 exomes
AF:
0.00303
AC:
527
AN:
173958
Hom.:
2
AF XY:
0.00297
AC XY:
284
AN XY:
95574
show subpopulations
Gnomad AFR exome
AF:
0.000735
Gnomad AMR exome
AF:
0.00117
Gnomad ASJ exome
AF:
0.00117
Gnomad EAS exome
AF:
0.000146
Gnomad SAS exome
AF:
0.000730
Gnomad FIN exome
AF:
0.00166
Gnomad NFE exome
AF:
0.00585
Gnomad OTH exome
AF:
0.00128
GnomAD4 exome
AF:
0.00541
AC:
7686
AN:
1419900
Hom.:
21
Cov.:
30
AF XY:
0.00528
AC XY:
3718
AN XY:
703632
show subpopulations
Gnomad4 AFR exome
AF:
0.00108
Gnomad4 AMR exome
AF:
0.00121
Gnomad4 ASJ exome
AF:
0.00189
Gnomad4 EAS exome
AF:
0.0000527
Gnomad4 SAS exome
AF:
0.000801
Gnomad4 FIN exome
AF:
0.00169
Gnomad4 NFE exome
AF:
0.00651
Gnomad4 OTH exome
AF:
0.00468
GnomAD4 genome
AF:
0.00339
AC:
516
AN:
152382
Hom.:
2
Cov.:
33
AF XY:
0.00313
AC XY:
233
AN XY:
74520
show subpopulations
Gnomad4 AFR
AF:
0.000914
Gnomad4 AMR
AF:
0.00216
Gnomad4 ASJ
AF:
0.00259
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00207
Gnomad4 FIN
AF:
0.00150
Gnomad4 NFE
AF:
0.00595
Gnomad4 OTH
AF:
0.00237
Alfa
AF:
0.00399
Hom.:
0
Bravo
AF:
0.00329
Asia WGS
AF:
0.000289
AC:
1
AN:
3478

ClinVar

Significance: Benign/Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:2
Benign, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpDec 31, 2019- -
Likely benign, criteria provided, single submitterclinical testingCeGaT Center for Human Genetics TuebingenJun 01, 2024ADAT3: BP4, BP7, BS2; SCAMP4: BS2 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
0.11
DANN
Benign
0.74

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs199915192; hg19: chr19-1912163; API