20-63861682-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4

The NM_080622.4(ABHD16B):​c.142C>T​(p.Arg48Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000444 in 1,530,078 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 Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R48Q) has been classified as Uncertain significance.

Frequency

Genomes: 𝑓 0.000059 ( 0 hom., cov: 31)
Exomes 𝑓: 0.000043 ( 0 hom. )

Consequence

ABHD16B
NM_080622.4 missense

Scores

1
5
13

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 0.0950
Variant links:
Genes affected
ABHD16B (HGNC:16128): (abhydrolase domain containing 16B) Predicted to enable acylglycerol lipase activity; palmitoyl-(protein) hydrolase activity; and phospholipase activity. Predicted to be involved in monoacylglycerol catabolic process and phosphatidylserine catabolic process. Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 1 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.34963447).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ABHD16BNM_080622.4 linkc.142C>T p.Arg48Trp missense_variant Exon 1 of 1 ENST00000369916.5 NP_542189.1 Q9H3Z7

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ABHD16BENST00000369916.5 linkc.142C>T p.Arg48Trp missense_variant Exon 1 of 1 6 NM_080622.4 ENSP00000358932.3 Q9H3Z7
ENSG00000268858ENST00000601296.2 linkn.2612G>A non_coding_transcript_exon_variant Exon 1 of 1 6

Frequencies

GnomAD3 genomes
AF:
0.0000593
AC:
9
AN:
151870
Hom.:
0
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.0000725
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000883
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.0000306
AC:
4
AN:
130778
Hom.:
0
AF XY:
0.0000140
AC XY:
1
AN XY:
71478
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000800
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.0000428
AC:
59
AN:
1378208
Hom.:
0
Cov.:
32
AF XY:
0.0000456
AC XY:
31
AN XY:
680160
show subpopulations
Gnomad4 AFR exome
AF:
0.0000327
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000494
Gnomad4 OTH exome
AF:
0.0000698
GnomAD4 genome
AF:
0.0000593
AC:
9
AN:
151870
Hom.:
0
Cov.:
31
AF XY:
0.0000674
AC XY:
5
AN XY:
74212
show subpopulations
Gnomad4 AFR
AF:
0.0000725
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000883
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.000234
Hom.:
0
Bravo
AF:
0.0000567

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Jun 30, 2023
Ambry Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The c.142C>T (p.R48W) alteration is located in exon 1 (coding exon 1) of the ABHD16B gene. This alteration results from a C to T substitution at nucleotide position 142, causing the arginine (R) at amino acid position 48 to be replaced by a tryptophan (W). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.12
BayesDel_addAF
Benign
-0.24
T
BayesDel_noAF
Benign
-0.39
CADD
Benign
17
DANN
Uncertain
1.0
DEOGEN2
Benign
0.010
T
Eigen
Benign
-0.070
Eigen_PC
Benign
-0.24
FATHMM_MKL
Benign
0.18
N
LIST_S2
Benign
0.71
T
M_CAP
Uncertain
0.14
D
MetaRNN
Benign
0.35
T
MetaSVM
Benign
-0.93
T
MutationAssessor
Uncertain
2.2
M
PrimateAI
Pathogenic
0.89
D
PROVEAN
Uncertain
-2.4
N
REVEL
Benign
0.21
Sift
Benign
0.030
D
Sift4G
Uncertain
0.055
T
Polyphen
1.0
D
Vest4
0.43
MutPred
0.50
Loss of disorder (P = 0.0099);
MVP
0.49
MPC
1.3
ClinPred
0.36
T
GERP RS
4.3
Varity_R
0.064
gMVP
0.55

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: rs965671960; hg19: chr20-62493035; COSMIC: COSV53861597; COSMIC: COSV53861597; API