rs12407294

Variant names:

• chr1-101235876-T-C
• rs12407294
• ENST00000432195.3:n.332A>G

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000432195.3(S1PR1-DT):​n.332A>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 ENST00000432195.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.645
• Publications: 9 publications found

Genes affected

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

ENSG00000306729 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
S1PR1-DT	NR_104626.1	n.210A>G		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
S1PR1-DT	ENST00000432195.3	n.332A>G		non_coding_transcript_exon_variant	Exon 2 of 2	2
S1PR1-DT	ENST00000686331.3	n.940A>G		non_coding_transcript_exon_variant	Exon 1 of 1
S1PR1-DT	ENST00000820226.1	n.749A>G		non_coding_transcript_exon_variant	Exon 1 of 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

African (AFR) AF: 0.500 AC: 1 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.625 AC: 5 AN: 8

South Asian (SAS) AF: 0.00 AC: 0 AN: 2

European-Finnish (FIN) AF: 0.833 AC: 5 AN: 6

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.303 AC: 23 AN: 76

Other (OTH) AF: 0.500 AC: 2 AN: 4

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

African (AFR) AF: 0.170 AC: 7048 AN: 41380

American (AMR) AF: 0.308 AC: 4687 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.333 AC: 1154 AN: 3468

East Asian (EAS) AF: 0.400 AC: 2058 AN: 5140

South Asian (SAS) AF: 0.325 AC: 1562 AN: 4802

European-Finnish (FIN) AF: 0.294 AC: 3097 AN: 10518

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.343 AC: 23272 AN: 67914

Other (OTH) AF: 0.305 AC: 643 AN: 2108

Alfa AF: 0.329 Hom.: 16000

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
PhyloP100		-0.65

Splicing

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

Other links and lift over

dbSNP: rs12407294; hg19: chr1-101701432;