chr1-101236367-C-G

Position:

• chr1-101236367-C-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.162G>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 0.37 in 152,190 control chromosomes in the GnomAD database, including 10,822 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 0.37 (10801 hom., cov: 30)
  • Exomes 𝑓: 0.32 (21 hom.)
• Consequence: S1PR1-DT NR_104626.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.99

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=-0.69).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.413 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
S1PR1-DT	NR_104626.1	n.162G>C		non_coding_transcript_exon_variant	1/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
S1PR1-DT	ENST00000686331.2	n.258G>C		non_coding_transcript_exon_variant	1/1
S1PR1-DT	ENST00000432195.2	n.258G>C		non_coding_transcript_exon_variant	1/2	2

Frequencies

GnomAD3 genomes AF: 0.370 AC: 56103 AN: 151686 Hom.: 10797 Cov.: 30

Gnomad AFR AF: 0.419

Gnomad AMI AF: 0.362

Gnomad AMR AF: 0.300

Gnomad ASJ AF: 0.329

Gnomad EAS AF: 0.118

Gnomad SAS AF: 0.414

Gnomad FIN AF: 0.373

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.374

Gnomad OTH AF: 0.355

GnomAD4 exome AF: 0.318 AC: 122 AN: 384 Hom.: 21 Cov.: 0 AF XY: 0.316 AC XY: 93 AN XY: 294

Gnomad4 AFR exome AF: 0.200

Gnomad4 AMR exome AF: 0.250

Gnomad4 ASJ exome AF: 0.500

Gnomad4 EAS exome AF: 0.0556

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.438

Gnomad4 NFE exome AF: 0.340

Gnomad4 OTH exome AF: 0.0833

GnomAD4 genome AF: 0.370 AC: 56122 AN: 151806 Hom.: 10801 Cov.: 30 AF XY: 0.366 AC XY: 27160 AN XY: 74188

Gnomad4 AFR AF: 0.418

Gnomad4 AMR AF: 0.299

Gnomad4 ASJ AF: 0.329

Gnomad4 EAS AF: 0.117

Gnomad4 SAS AF: 0.415

Gnomad4 FIN AF: 0.373

Gnomad4 NFE AF: 0.374

Gnomad4 OTH AF: 0.351

Alfa AF: 0.260 Hom.: 649

Bravo AF: 0.361

Asia WGS AF: 0.290 AC: 1009 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	1.6
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs59317557; hg19: chr1-101701923;