chr1-101243017-GA-G

Variant names:

• chr1-101243017-GA-G
• rs35079261
• ENST00000561748.2:n.1282delA

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The ENST00000561748.2(S1PR1):​n.1282delA 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
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
S1PR1	ENST00000561748.2	n.1282delA		non_coding_transcript_exon_variant	Exon 3 of 3	6

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

African (AFR) AF: 0.135 AC: 5602 AN: 41460

American (AMR) AF: 0.109 AC: 1660 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.106 AC: 369 AN: 3468

East Asian (EAS) AF: 0.421 AC: 2183 AN: 5180

South Asian (SAS) AF: 0.0735 AC: 354 AN: 4816

European-Finnish (FIN) AF: 0.159 AC: 1680 AN: 10550

Middle Eastern (MID) AF: 0.103 AC: 30 AN: 292

European-Non Finnish (NFE) AF: 0.0904 AC: 6142 AN: 67946

Other (OTH) AF: 0.109 AC: 230 AN: 2112

Alfa AF: 0.103 Hom.: 90

Bravo AF: 0.123

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs35079261; hg19: chr1-101708573;