chr10-70914732-C-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000697990.2(SGPL1):​c.465-39487C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.425 in 152,088 control chromosomes in the GnomAD database, including 14,995 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 0.43 ( 14995 hom., cov: 32)

Consequence

SGPL1
ENST00000697990.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.827

Publications

1 publications found
Variant links:
Genes affected
SGPL1 (HGNC:10817): (sphingosine-1-phosphate lyase 1) Enables sphinganine-1-phosphate aldolase activity. Involved in apoptotic signaling pathway; fatty acid metabolic process; and sphingolipid metabolic process. Located in endoplasmic reticulum. Implicated in nephrotic syndrome type 14. [provided by Alliance of Genome Resources, Apr 2022]
SGPL1 Gene-Disease associations (from GenCC):
  • nephrotic syndrome 14
    Inheritance: AR Classification: STRONG, MODERATE Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae), PanelApp Australia

Genome browser will be placed here

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=-0.91).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.515 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SGPL1ENST00000697990.2 linkc.465-39487C>T intron_variant Intron 7 of 7 ENSP00000520631.1

Frequencies

GnomAD3 genomes
AF:
0.426
AC:
64686
AN:
151970
Hom.:
14998
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.235
Gnomad AMI
AF:
0.370
Gnomad AMR
AF:
0.524
Gnomad ASJ
AF:
0.463
Gnomad EAS
AF:
0.386
Gnomad SAS
AF:
0.503
Gnomad FIN
AF:
0.470
Gnomad MID
AF:
0.465
Gnomad NFE
AF:
0.509
Gnomad OTH
AF:
0.421
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.425
AC:
64694
AN:
152088
Hom.:
14995
Cov.:
32
AF XY:
0.426
AC XY:
31652
AN XY:
74346
show subpopulations
African (AFR)
AF:
0.235
AC:
9764
AN:
41500
American (AMR)
AF:
0.524
AC:
8011
AN:
15284
Ashkenazi Jewish (ASJ)
AF:
0.463
AC:
1604
AN:
3466
East Asian (EAS)
AF:
0.385
AC:
1988
AN:
5162
South Asian (SAS)
AF:
0.503
AC:
2424
AN:
4818
European-Finnish (FIN)
AF:
0.470
AC:
4974
AN:
10584
Middle Eastern (MID)
AF:
0.449
AC:
132
AN:
294
European-Non Finnish (NFE)
AF:
0.509
AC:
34583
AN:
67962
Other (OTH)
AF:
0.416
AC:
877
AN:
2106
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
1817
3634
5451
7268
9085
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
612
1224
1836
2448
3060
<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:
0.485
Hom.:
33657
Bravo
AF:
0.422
Asia WGS
AF:
0.411
AC:
1428
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
2.1
DANN
Benign
0.76
PhyloP100
-0.83

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs12415816; hg19: chr10-72674489; API