chr16-68400980-A-G
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_018667.4(SMPD3):c.-268-14321T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.511 in 152,056 control chromosomes in the GnomAD database, including 21,785 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.51 ( 21785 hom., cov: 32)
Consequence
SMPD3
NM_018667.4 intron
NM_018667.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.863
Publications
11 publications found
Genes affected
SMPD3 (HGNC:14240): (sphingomyelin phosphodiesterase 3) Predicted to enable phosphatidic acid binding activity; phosphatidylserine binding activity; and sphingomyelin phosphodiesterase activity. Predicted to be involved in positive regulation of exosomal secretion and sphingomyelin metabolic process. Predicted to act upstream of or within several processes, including animal organ development; enzyme linked receptor protein signaling pathway; and sphingolipid metabolic process. Predicted to be located in Golgi apparatus and plasma membrane. Predicted to be active in cytoplasm. Biomarker of pulmonary emphysema. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.71).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.839 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SMPD3 | ENST00000219334.10 | c.-268-14321T>C | intron_variant | Intron 1 of 8 | 1 | NM_018667.4 | ENSP00000219334.5 | |||
SMPD3 | ENST00000561749.1 | c.-206-28593T>C | intron_variant | Intron 1 of 1 | 2 | ENSP00000457236.1 | ||||
SMPD3 | ENST00000566723.1 | n.91-14321T>C | intron_variant | Intron 1 of 4 | 4 |
Frequencies
GnomAD3 genomes AF: 0.511 AC: 77697AN: 151938Hom.: 21771 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
77697
AN:
151938
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.511 AC: 77737AN: 152056Hom.: 21785 Cov.: 32 AF XY: 0.512 AC XY: 38034AN XY: 74344 show subpopulations
GnomAD4 genome
AF:
AC:
77737
AN:
152056
Hom.:
Cov.:
32
AF XY:
AC XY:
38034
AN XY:
74344
show subpopulations
African (AFR)
AF:
AC:
12140
AN:
41472
American (AMR)
AF:
AC:
10323
AN:
15276
Ashkenazi Jewish (ASJ)
AF:
AC:
1868
AN:
3472
East Asian (EAS)
AF:
AC:
4454
AN:
5178
South Asian (SAS)
AF:
AC:
2654
AN:
4818
European-Finnish (FIN)
AF:
AC:
4887
AN:
10566
Middle Eastern (MID)
AF:
AC:
156
AN:
294
European-Non Finnish (NFE)
AF:
AC:
39530
AN:
67966
Other (OTH)
AF:
AC:
1200
AN:
2106
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.499
Heterozygous variant carriers
0
1800
3599
5399
7198
8998
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
686
1372
2058
2744
3430
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
2244
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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