Variant rs6511701 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_030760.5(S1PR5):c.621T>G(p.Ala207=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.791 in 1,602,702 control chromosomes in the GnomAD database, including 502,913 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 0.79 ( 47724 hom., cov: 35)

Exomes 𝑓: 0.79 ( 455189 hom. )

Consequence

S1PR5
NM_030760.5 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.93

Variant links:

Genes affected

S1PR5 (HGNC:14299): (sphingosine-1-phosphate receptor 5) The lysosphingolipid sphingosine 1-phosphate (S1P) regulates cell proliferation, apoptosis, motility, and neurite retraction. Its actions may be both intracellular as a second messenger and extracellular as a receptor ligand. S1P and the structurally related lysolipid mediator lysophosphatidic acid (LPA) signal cells through a set of G protein-coupled receptors known as EDG receptors. Some EDG receptors (e.g., EDG1; MIM 601974) are S1P receptors; others (e.g., EDG2; MIM 602282) are LPA receptors.[supplied by OMIM, Mar 2008]

S1PR5 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.73).

BP7

Synonymous conserved (PhyloP=1.93 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.872 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
S1PR5	NM_030760.5 linkuse as main transcript	c.621T>G	p.Ala207=	synonymous_variant	2/2	ENST00000333430.6
S1PR5	NM_001166215.2 linkuse as main transcript	c.621T>G	p.Ala207=	synonymous_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
S1PR5	ENST00000333430.6 linkuse as main transcript	c.621T>G	p.Ala207=	synonymous_variant	2/2	1	NM_030760.5	P1	Q9H228-1
S1PR5	ENST00000439028.3 linkuse as main transcript	c.621T>G	p.Ala207=	synonymous_variant	2/2	2		P1	Q9H228-1

Frequencies

GnomAD3 genomes

AF:

0.790

AC:

120221

AN:

152084

Hom.:

47680

Cov.:

show subpopulations

Gnomad AFR

AF:

0.776

Gnomad AMI

AF:

0.720

Gnomad AMR

AF:

0.830

Gnomad ASJ

AF:

0.748

Gnomad EAS

AF:

0.779

Gnomad SAS

AF:

0.894

Gnomad FIN

AF:

0.800

Gnomad MID

AF:

0.707

Gnomad NFE

AF:

0.786

Gnomad OTH

AF:

0.783

GnomAD3 exomes

AF:

0.805

AC:

183390

AN:

227918

Hom.:

74035

AF XY:

0.807

AC XY:

100162

AN XY:

124172

show subpopulations

Gnomad AFR exome

AF:

0.770

Gnomad AMR exome

AF:

0.863

Gnomad ASJ exome

AF:

0.750

Gnomad EAS exome

AF:

0.767

Gnomad SAS exome

AF:

0.888

Gnomad FIN exome

AF:

0.808

Gnomad NFE exome

AF:

0.779

Gnomad OTH exome

AF:

0.790

GnomAD4 exome

AF:

0.791

AC:

1147930

AN:

1450506

Hom.:

455189

Cov.:

AF XY:

0.793

AC XY:

571779

AN XY:

720590

show subpopulations

Gnomad4 AFR exome

AF:

0.776

Gnomad4 AMR exome

AF:

0.860

Gnomad4 ASJ exome

AF:

0.755

Gnomad4 EAS exome

AF:

0.829

Gnomad4 SAS exome

AF:

0.886

Gnomad4 FIN exome

AF:

0.807

Gnomad4 NFE exome

AF:

0.781

Gnomad4 OTH exome

AF:

0.787

GnomAD4 genome

AF:

0.791

AC:

120319

AN:

152196

Hom.:

47724

Cov.:

AF XY:

0.793

AC XY:

59019

AN XY:

74390

show subpopulations

Gnomad4 AFR

AF:

0.776

Gnomad4 AMR

AF:

0.830

Gnomad4 ASJ

AF:

0.748

Gnomad4 EAS

AF:

0.779

Gnomad4 SAS

AF:

0.894

Gnomad4 FIN

AF:

0.800

Gnomad4 NFE

AF:

0.786

Gnomad4 OTH

AF:

0.784

Alfa

AF:

0.773

Hom.:

16322

Bravo

AF:

0.789

Asia WGS

AF:

0.864

AC:

3002

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.73

CADD

Benign

8.4

DANN

Benign

0.26

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over