17-29566402-C-A
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Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_198147.3(ABHD15):c.565G>T(p.Val189Phe) variant causes a missense change. The variant allele was found at a frequency of 0.00000274 in 1,459,362 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 0.0000027 ( 0 hom. )
Consequence
ABHD15
NM_198147.3 missense
NM_198147.3 missense
Scores
7
10
2
Clinical Significance
Conservation
PhyloP100: 3.71
Genes affected
ABHD15 (HGNC:26971): (abhydrolase domain containing 15) Predicted to enable acylglycerol lipase activity and short-chain carboxylesterase activity. Predicted to be involved in cellular lipid metabolic process. Located in membrane. [provided by Alliance of Genome Resources, Apr 2022]
ABHD15-AS1 (HGNC:49685): (ABHD15 antisense RNA 1)
TP53I13 (HGNC:25102): (tumor protein p53 inducible protein 13) Involved in several processes, including negative regulation of cell cycle; response to UV; and response to xenobiotic stimulus. Located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 4 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.84
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ABHD15 | NM_198147.3 | c.565G>T | p.Val189Phe | missense_variant | 1/2 | ENST00000307201.5 | NP_937790.2 | |
TP53I13 | XM_047437003.1 | c.-461C>A | 5_prime_UTR_variant | 1/8 | XP_047292959.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ABHD15 | ENST00000307201.5 | c.565G>T | p.Val189Phe | missense_variant | 1/2 | 1 | NM_198147.3 | ENSP00000302657 | P1 | |
ABHD15-AS1 | ENST00000581474.1 | n.153+5703C>A | intron_variant, non_coding_transcript_variant | 5 | ||||||
TP53I13 | ENST00000584522.1 | n.102C>A | non_coding_transcript_exon_variant | 1/2 | 4 | |||||
TP53I13 | ENST00000578073.1 | n.177+174C>A | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 genomes
Cov.:
33
GnomAD3 exomes AF: 0.0000123 AC: 3AN: 244234Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 133676
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GnomAD4 exome AF: 0.00000274 AC: 4AN: 1459362Hom.: 0 Cov.: 32 AF XY: 0.00000138 AC XY: 1AN XY: 725838
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GnomAD4 genome Cov.: 33
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 22, 2021 | The c.565G>T (p.V189F) alteration is located in exon 1 (coding exon 1) of the ABHD15 gene. This alteration results from a G to T substitution at nucleotide position 565, causing the valine (V) at amino acid position 189 to be replaced by a phenylalanine (F). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
CADD
Pathogenic
DANN
Uncertain
DEOGEN2
Benign
T
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D
M_CAP
Uncertain
D
MetaRNN
Pathogenic
D
MetaSVM
Uncertain
D
MutationAssessor
Uncertain
M
MutationTaster
Benign
D
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D
REVEL
Uncertain
Sift
Pathogenic
D
Sift4G
Uncertain
D
Polyphen
D
Vest4
MutPred
Gain of methylation at R184 (P = 0.2185);
MVP
MPC
ClinPred
D
GERP RS
Varity_R
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