chr19-3179077-G-A

Variant summary

Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2

The NM_003775.4(S1PR4):​c.285G>A​(p.Thr95=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00671 in 1,610,354 control chromosomes in the GnomAD database, including 54 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0053 ( 5 hom., cov: 33)
Exomes 𝑓: 0.0069 ( 49 hom. )

Consequence

S1PR4
NM_003775.4 synonymous

Scores

2

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -4.50
Variant links:
Genes affected
S1PR4 (HGNC:3170): (sphingosine-1-phosphate receptor 4) This gene is a member of the endothelial differentiation, G-protein-coupled (EDG)) receptor gene family. EDG receptors bind lysophospholipids or lysosphingolipids as ligands, and are involved in cell signalling in many different cell types. This EDG receptor gene is intronless and is specifically expressed in the lymphoid tissue. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -17 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.48).
BP6
Variant 19-3179077-G-A is Benign according to our data. Variant chr19-3179077-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 771510.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=-4.5 with no splicing effect.
BS2
High Homozygotes in GnomAd4 at 5 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
S1PR4NM_003775.4 linkuse as main transcriptc.285G>A p.Thr95= synonymous_variant 1/1 ENST00000246115.5

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
S1PR4ENST00000246115.5 linkuse as main transcriptc.285G>A p.Thr95= synonymous_variant 1/1 NM_003775.4 P1
S1PR4ENST00000591346.1 linkuse as main transcriptn.100-137G>A intron_variant, non_coding_transcript_variant 3

Frequencies

GnomAD3 genomes
AF:
0.00535
AC:
814
AN:
152212
Hom.:
5
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.00111
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00294
Gnomad ASJ
AF:
0.00346
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00497
Gnomad FIN
AF:
0.0139
Gnomad MID
AF:
0.0158
Gnomad NFE
AF:
0.00767
Gnomad OTH
AF:
0.00573
GnomAD3 exomes
AF:
0.00668
AC:
1598
AN:
239048
Hom.:
11
AF XY:
0.00689
AC XY:
902
AN XY:
130996
show subpopulations
Gnomad AFR exome
AF:
0.00125
Gnomad AMR exome
AF:
0.00364
Gnomad ASJ exome
AF:
0.00380
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00473
Gnomad FIN exome
AF:
0.0126
Gnomad NFE exome
AF:
0.00924
Gnomad OTH exome
AF:
0.00792
GnomAD4 exome
AF:
0.00685
AC:
9993
AN:
1458024
Hom.:
49
Cov.:
32
AF XY:
0.00686
AC XY:
4974
AN XY:
725382
show subpopulations
Gnomad4 AFR exome
AF:
0.00105
Gnomad4 AMR exome
AF:
0.00401
Gnomad4 ASJ exome
AF:
0.00368
Gnomad4 EAS exome
AF:
0.000101
Gnomad4 SAS exome
AF:
0.00510
Gnomad4 FIN exome
AF:
0.0119
Gnomad4 NFE exome
AF:
0.00740
Gnomad4 OTH exome
AF:
0.00609
GnomAD4 genome
AF:
0.00533
AC:
812
AN:
152330
Hom.:
5
Cov.:
33
AF XY:
0.00542
AC XY:
404
AN XY:
74496
show subpopulations
Gnomad4 AFR
AF:
0.00108
Gnomad4 AMR
AF:
0.00294
Gnomad4 ASJ
AF:
0.00346
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00477
Gnomad4 FIN
AF:
0.0139
Gnomad4 NFE
AF:
0.00767
Gnomad4 OTH
AF:
0.00567
Alfa
AF:
0.00506
Hom.:
1
Bravo
AF:
0.00433
Asia WGS
AF:
0.00260
AC:
9
AN:
3478
EpiCase
AF:
0.00829
EpiControl
AF:
0.00848

ClinVar

Significance: Benign/Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:2
Likely benign, criteria provided, single submitterclinical testingCeGaT Center for Human Genetics TuebingenMar 01, 2023S1PR4: BP4, BP7, BS2 -
Benign, criteria provided, single submitterclinical testingInvitaeMay 02, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.48
CADD
Benign
0.20
DANN
Benign
0.97

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.020
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: rs34573539; hg19: chr19-3179075; API