rs35079261

Positions:

• chr1-101243017-GA-G
• chr1-101243017-GA-GAA

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The ENST00000561748.2(S1PR1):​n.1282del variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.121 in 152,024 control chromosomes in the GnomAD database, including 1,385 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.12 (1385 hom., cov: 30)
  • Failed GnomAD Quality Control
• Consequence: S1PR1 ENST00000561748.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.159

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 -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.407 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
S1PR1	ENST00000561748.2	n.1282del		non_coding_transcript_exon_variant	3/3

Frequencies

GnomAD3 genomes AF: 0.121 AC: 18370 AN: 151906 Hom.: 1388 Cov.: 30

Gnomad AFR AF: 0.135

Gnomad AMI AF: 0.133

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.106

Gnomad EAS AF: 0.422

Gnomad SAS AF: 0.0747

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.102

Gnomad NFE AF: 0.0904

Gnomad OTH AF: 0.110

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.121 AC: 18371 AN: 152024 Hom.: 1385 Cov.: 30 AF XY: 0.124 AC XY: 9189 AN XY: 74326

Gnomad4 AFR AF: 0.135

Gnomad4 AMR AF: 0.109

Gnomad4 ASJ AF: 0.106

Gnomad4 EAS AF: 0.421

Gnomad4 SAS AF: 0.0735

Gnomad4 FIN AF: 0.159

Gnomad4 NFE AF: 0.0904

Gnomad4 OTH AF: 0.109

Alfa AF: 0.103 Hom.: 90

Bravo AF: 0.123

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs35079261; hg19: chr1-101708573;