rs61780687

chr1-101238092-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001400.5(S1PR1):c.-163-730A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.255 in 151,778 control chromosomes in the GnomAD database, including 6,166 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 0.26 (6159 hom., cov: 29)
  • Exomes 𝑓: 0.37 (7 hom.)
• Consequence: S1PR1 NM_001400.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.714

Genes affected

S1PR1 (HGNC:3165): (sphingosine-1-phosphate receptor 1) The protein encoded by this gene is structurally similar to G protein-coupled receptors and is highly expressed in endothelial cells. It binds the ligand sphingosine-1-phosphate with high affinity and high specificity, and suggested to be involved in the processes that regulate the differentiation of endothelial cells. Activation of this receptor induces cell-cell adhesion. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2016]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.362 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
S1PR1	NM_001400.5	c.-163-730A>T		intron_variant		ENST00000305352.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
S1PR1	ENST00000305352.7	c.-163-730A>T		intron_variant		1	NM_001400.5	P1

Frequencies

GnomAD3 genomes AF: 0.255 AC: 38718 AN: 151586 Hom.: 6157 Cov.: 29

Gnomad AFR AF: 0.0942

Gnomad AMI AF: 0.281

Gnomad AMR AF: 0.229

Gnomad ASJ AF: 0.244

Gnomad EAS AF: 0.0568

Gnomad SAS AF: 0.264

Gnomad FIN AF: 0.311

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.366

Gnomad OTH AF: 0.254

GnomAD4 exome AF: 0.369 AC: 31 AN: 84 Hom.: 7 Cov.: 0 AF XY: 0.351 AC XY: 26 AN XY: 74

Gnomad4 AFR exome AF: 0.250

Gnomad4 EAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.414

Gnomad4 OTH exome AF: 0.250

GnomAD4 genome AF: 0.255 AC: 38727 AN: 151694 Hom.: 6159 Cov.: 29 AF XY: 0.250 AC XY: 18563 AN XY: 74112

Gnomad4 AFR AF: 0.0942

Gnomad4 AMR AF: 0.228

Gnomad4 ASJ AF: 0.244

Gnomad4 EAS AF: 0.0570

Gnomad4 SAS AF: 0.266

Gnomad4 FIN AF: 0.311

Gnomad4 NFE AF: 0.366

Gnomad4 OTH AF: 0.252

Alfa AF: 0.300 Hom.: 920

Bravo AF: 0.239

Asia WGS AF: 0.152 AC: 533 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
Cadd	Benign	14
Dann	Benign	0.88

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

Other links and lift over

dbSNP: rs61780687; hg19: chr1-101703648;