rs2883990

chr14-63690399-T-C

Variant summary

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

The NM_030791.4(SGPP1):c.775-3743A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.22 in 152,186 control chromosomes in the GnomAD database, including 4,054 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 0.22 (4054 hom., cov: 33)
• Consequence: SGPP1 NM_030791.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.641

Genes affected

SGPP1 (HGNC:17720): (sphingosine-1-phosphate phosphatase 1) Sphingosine-1-phosphate (S1P) is a bioactive sphingolipid metabolite that regulates diverse biologic processes. SGPP1 catalyzes the degradation of S1P via salvage and recycling of sphingosine into long-chain ceramides (Mandala et al., 2000 [PubMed 10859351]; Le Stunff et al., 2007 [PubMed 17895250]).[supplied by OMIM, Jun 2009]

LOC124903327 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.483 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SGPP1	NM_030791.4	c.775-3743A>G		intron_variant		ENST00000247225.7
LOC124903327	XR_007064204.1	n.125T>C		non_coding_transcript_exon_variant	1/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SGPP1	ENST00000247225.7	c.775-3743A>G		intron_variant		1	NM_030791.4	P1

Frequencies

GnomAD3 genomes AF: 0.221 AC: 33570 AN: 152068 Hom.: 4064 Cov.: 33

Gnomad AFR AF: 0.175

Gnomad AMI AF: 0.292

Gnomad AMR AF: 0.245

Gnomad ASJ AF: 0.270

Gnomad EAS AF: 0.500

Gnomad SAS AF: 0.272

Gnomad FIN AF: 0.204

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.217

Gnomad OTH AF: 0.229

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.220 AC: 33547 AN: 152186 Hom.: 4054 Cov.: 33 AF XY: 0.224 AC XY: 16684 AN XY: 74396

Gnomad4 AFR AF: 0.175

Gnomad4 AMR AF: 0.245

Gnomad4 ASJ AF: 0.270

Gnomad4 EAS AF: 0.499

Gnomad4 SAS AF: 0.269

Gnomad4 FIN AF: 0.204

Gnomad4 NFE AF: 0.217

Gnomad4 OTH AF: 0.228

Alfa AF: 0.217 Hom.: 2123

Bravo AF: 0.224

Asia WGS AF: 0.359 AC: 1246 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	4.1
Dann	Benign	0.79

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs2883990; hg19: chr14-64157117;