chr1-101235925-T-C

Position:

• chr1-101235925-T-C

Variant summary

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

The ENST00000686331.2(S1PR1-DT):​n.700A>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 0.342 in 151,808 control chromosomes in the GnomAD database, including 9,293 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 0.34 (9293 hom., cov: 30)
  • Exomes 𝑓: 0.28 (0 hom.)
• Consequence: S1PR1-DT ENST00000686331.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.230

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=-0.82).
• 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	Protein	UniProt
S1PR1-DT	NR_104626.1	n.205-44A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
S1PR1-DT	ENST00000686331.2	n.700A>G		non_coding_transcript_exon_variant	1/1
S1PR1-DT	ENST00000432195.2	n.301-44A>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.342 AC: 51812 AN: 151672 Hom.: 9286 Cov.: 30

Gnomad AFR AF: 0.418

Gnomad AMI AF: 0.351

Gnomad AMR AF: 0.263

Gnomad ASJ AF: 0.262

Gnomad EAS AF: 0.127

Gnomad SAS AF: 0.415

Gnomad FIN AF: 0.346

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.328

Gnomad OTH AF: 0.318

GnomAD4 exome AF: 0.278 AC: 5 AN: 18 Hom.: 0 Cov.: 0 AF XY: 0.250 AC XY: 3 AN XY: 12

Gnomad4 EAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.250

GnomAD4 genome AF: 0.342 AC: 51839 AN: 151790 Hom.: 9293 Cov.: 30 AF XY: 0.339 AC XY: 25181 AN XY: 74186

Gnomad4 AFR AF: 0.418

Gnomad4 AMR AF: 0.263

Gnomad4 ASJ AF: 0.262

Gnomad4 EAS AF: 0.127

Gnomad4 SAS AF: 0.416

Gnomad4 FIN AF: 0.346

Gnomad4 NFE AF: 0.328

Gnomad4 OTH AF: 0.314

Alfa AF: 0.314 Hom.: 3646

Bravo AF: 0.332

Asia WGS AF: 0.288 AC: 1000 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	8.1
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs33967958; hg19: chr1-101701481;