1-101241570-T-C

Position:

• chr1-101241570-T-C

Variant summary

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

The XR_007095678.1(S1PR1):​n.2830T>C 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 0.136 in 165,572 control chromosomes in the GnomAD database, including 2,430 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 0.14 (2351 hom., cov: 32)
  • Exomes 𝑓: 0.10 (79 hom.)
• Consequence: S1PR1 XR_007095678.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.590

Genes affected

S1PR1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.267 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
S1PR1	XR_007095678.1	n.2830T>C		non_coding_transcript_exon_variant	2/3
S1PR1	NR_174345.1	n.82-119T>C		intron_variant
S1PR1	NR_174346.1	n.82-458T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
S1PR1	ENST00000561748.2	n.202-119T>C		intron_variant		6

Frequencies

GnomAD3 genomes AF: 0.139 AC: 21064 AN: 152008 Hom.: 2335 Cov.: 32

Gnomad AFR AF: 0.271

Gnomad AMI AF: 0.0866

Gnomad AMR AF: 0.265

Gnomad ASJ AF: 0.0494

Gnomad EAS AF: 0.0880

Gnomad SAS AF: 0.0507

Gnomad FIN AF: 0.0993

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0522

Gnomad OTH AF: 0.115

GnomAD4 exome AF: 0.102 AC: 1375 AN: 13446 Hom.: 79 AF XY: 0.103 AC XY: 659 AN XY: 6414

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.500

Gnomad4 EAS exome AF: 0.0845

Gnomad4 FIN exome AF: 0.103

Gnomad4 NFE exome AF: 0.0789

Gnomad4 OTH exome AF: 0.0625

GnomAD4 genome AF: 0.139 AC: 21116 AN: 152126 Hom.: 2351 Cov.: 32 AF XY: 0.142 AC XY: 10529 AN XY: 74380

Gnomad4 AFR AF: 0.271

Gnomad4 AMR AF: 0.266

Gnomad4 ASJ AF: 0.0494

Gnomad4 EAS AF: 0.0878

Gnomad4 SAS AF: 0.0507

Gnomad4 FIN AF: 0.0993

Gnomad4 NFE AF: 0.0522

Gnomad4 OTH AF: 0.114

Alfa AF: 0.0897 Hom.: 267

Bravo AF: 0.162

Asia WGS AF: 0.0860 AC: 295 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.79
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12090529; hg19: chr1-101707126;