chr19-49461915-G-A
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Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_153329.4(ALDH16A1):c.791G>A(p.Gly264Glu) variant causes a missense change. The variant allele was found at a frequency of 0.000357 in 1,580,888 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0018 ( 1 hom., cov: 33)
Exomes 𝑓: 0.00021 ( 0 hom. )
Consequence
ALDH16A1
NM_153329.4 missense
NM_153329.4 missense
Scores
2
11
6
Clinical Significance
Conservation
PhyloP100: 4.71
Genes affected
ALDH16A1 (HGNC:28114): (aldehyde dehydrogenase 16 family member A1) This gene encodes a member of the aldehyde dehydrogenase superfamily. The family members act on aldehyde substrates and use nicotinamide adenine dinucleotide phosphate (NADP) as a cofactor. This gene is conserved in chimpanzee, dog, cow, mouse, rat, and zebrafish. The protein encoded by this gene interacts with maspardin, a protein that when truncated is responsible for Mast syndrome. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Apr 2010]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.014759004).
BP6
Variant 19-49461915-G-A is Benign according to our data. Variant chr19-49461915-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 729212.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ALDH16A1 | NM_153329.4 | c.791G>A | p.Gly264Glu | missense_variant | 7/17 | ENST00000293350.9 | |
ALDH16A1 | XM_011526441.1 | c.704G>A | p.Gly235Glu | missense_variant | 7/17 | ||
ALDH16A1 | XM_047438163.1 | c.704G>A | p.Gly235Glu | missense_variant | 8/18 | ||
ALDH16A1 | NM_001145396.2 | c.759+115G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ALDH16A1 | ENST00000293350.9 | c.791G>A | p.Gly264Glu | missense_variant | 7/17 | 1 | NM_153329.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00176 AC: 267AN: 151842Hom.: 1 Cov.: 33
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GnomAD3 exomes AF: 0.000507 AC: 99AN: 195402Hom.: 0 AF XY: 0.000395 AC XY: 42AN XY: 106316
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GnomAD4 exome AF: 0.000208 AC: 297AN: 1428926Hom.: 0 Cov.: 60 AF XY: 0.000176 AC XY: 125AN XY: 708416
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GnomAD4 genome AF: 0.00176 AC: 268AN: 151962Hom.: 1 Cov.: 33 AF XY: 0.00179 AC XY: 133AN XY: 74316
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 04, 2017 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Uncertain
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
T;T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Benign
D
LIST_S2
Benign
T;T
M_CAP
Uncertain
D
MetaRNN
Benign
T;T
MetaSVM
Uncertain
T
MutationAssessor
Benign
L;.
MutationTaster
Benign
D;D;D;D
PrimateAI
Uncertain
T
PROVEAN
Pathogenic
D;D
REVEL
Uncertain
Sift
Uncertain
D;D
Sift4G
Uncertain
D;D
Polyphen
D;D
Vest4
MVP
MPC
ClinPred
T
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gMVP
Splicing
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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