rs12407294

Positions:

• chr1-101235876-T-C
• chr1-101235876-T-G

Variant summary

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

The NR_104626.1(S1PR1-DT):​n.210A>G 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 0.29 in 151,874 control chromosomes in the GnomAD database, including 6,819 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 0.29 (6813 hom., cov: 29)
  • Exomes 𝑓: 0.36 (6 hom.)
• Consequence: S1PR1-DT NR_104626.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.645

Genes affected

S1PR1-DT (HGNC:55842): (S1PR1 divergent transcript)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.386 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
S1PR1-DT	NR_104626.1	n.210A>G		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
S1PR1-DT	ENST00000686331.2	n.749A>G		non_coding_transcript_exon_variant	1/1
S1PR1-DT	ENST00000432195.2	n.306A>G		non_coding_transcript_exon_variant	2/2	2

Frequencies

GnomAD3 genomes AF: 0.290 AC: 43942 AN: 151656 Hom.: 6812 Cov.: 29

Gnomad AFR AF: 0.171

Gnomad AMI AF: 0.363

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.333

Gnomad EAS AF: 0.399

Gnomad SAS AF: 0.325

Gnomad FIN AF: 0.294

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.343

Gnomad OTH AF: 0.306

GnomAD4 exome AF: 0.360 AC: 36 AN: 100 Hom.: 6 Cov.: 0 AF XY: 0.395 AC XY: 30 AN XY: 76

Gnomad4 AFR exome AF: 0.500

Gnomad4 EAS exome AF: 0.625

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.833

Gnomad4 NFE exome AF: 0.303

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.289 AC: 43937 AN: 151774 Hom.: 6813 Cov.: 29 AF XY: 0.289 AC XY: 21430 AN XY: 74168

Gnomad4 AFR AF: 0.170

Gnomad4 AMR AF: 0.308

Gnomad4 ASJ AF: 0.333

Gnomad4 EAS AF: 0.400

Gnomad4 SAS AF: 0.325

Gnomad4 FIN AF: 0.294

Gnomad4 NFE AF: 0.343

Gnomad4 OTH AF: 0.305

Alfa AF: 0.334 Hom.: 11990

Bravo AF: 0.289

Asia WGS AF: 0.340 AC: 1184 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.4
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12407294; hg19: chr1-101701432;