rs7140
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_032038.3(SPNS1):c.*137C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.726 in 854,248 control chromosomes in the GnomAD database, including 229,198 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 0.77 ( 45475 hom., cov: 34)
Exomes 𝑓: 0.72 ( 183723 hom. )
Consequence
SPNS1
NM_032038.3 3_prime_UTR
NM_032038.3 3_prime_UTR
Scores
1
10
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.46
Genes affected
SPNS1 (HGNC:30621): (SPNS lysolipid transporter 1, lysophospholipid) Predicted to enable transmembrane transporter activity. Predicted to be involved in lipid transport and transmembrane transport. Located in lysosomal membrane. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=7.219226E-7).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.906 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SPNS1 | NM_032038.3 | c.*137C>A | 3_prime_UTR_variant | 12/12 | ENST00000311008.16 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SPNS1 | ENST00000311008.16 | c.*137C>A | 3_prime_UTR_variant | 12/12 | 1 | NM_032038.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.765 AC: 116330AN: 152056Hom.: 45424 Cov.: 34
GnomAD3 genomes
?
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116330
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34
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GnomAD3 exomes AF: 0.729 AC: 101296AN: 138880Hom.: 37943 AF XY: 0.739 AC XY: 55820AN XY: 75520
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GnomAD4 exome AF: 0.717 AC: 503712AN: 702074Hom.: 183723 Cov.: 9 AF XY: 0.722 AC XY: 267345AN XY: 370072
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GnomAD4 genome ? AF: 0.765 AC: 116427AN: 152174Hom.: 45475 Cov.: 34 AF XY: 0.764 AC XY: 56851AN XY: 74390
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2587
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2665
ExAC
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44792
Asia WGS
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2872
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3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
DEOGEN2
Benign
T
FATHMM_MKL
Benign
N
LIST_S2
Benign
T
MetaRNN
Benign
T
MutationTaster
Benign
P;P;P;P;P
PROVEAN
Benign
N
Sift
Pathogenic
D
Sift4G
Benign
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
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