16-28976948-C-T

Position:

• chr16-28976948-C-T

Variant summary

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

The NM_032038.3(SPNS1):​c.308-960C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.774 in 152,190 control chromosomes in the GnomAD database, including 46,703 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 0.77 (46703 hom., cov: 33)
• Consequence: SPNS1 NM_032038.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.711

Genes affected

SPNS1 (HGNC:30621): (SPNS lysolipid transporter 1, lysophospholipid) Predicted to enable transmembrane transporter activity. Predicted to be involved in lipid transport and transmembrane transport. Located in lysosomal membrane. [provided by Alliance of Genome Resources, Apr 2022]

SPNS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.935 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SPNS1	NM_032038.3	c.308-960C>T		intron_variant		ENST00000311008.16	NP_114427.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SPNS1	ENST00000311008.16	c.308-960C>T		intron_variant		1	NM_032038.3	ENSP00000309945.11

Frequencies

GnomAD3 genomes AF: 0.774 AC: 117677 AN: 152072 Hom.: 46650 Cov.: 33

Gnomad AFR AF: 0.943

Gnomad AMI AF: 0.760

Gnomad AMR AF: 0.660

Gnomad ASJ AF: 0.822

Gnomad EAS AF: 0.916

Gnomad SAS AF: 0.811

Gnomad FIN AF: 0.673

Gnomad MID AF: 0.858

Gnomad NFE AF: 0.696

Gnomad OTH AF: 0.785

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

GnomAD4 genome AF: 0.774 AC: 117776 AN: 152190 Hom.: 46703 Cov.: 33 AF XY: 0.773 AC XY: 57504 AN XY: 74394

Gnomad4 AFR AF: 0.943

Gnomad4 AMR AF: 0.659

Gnomad4 ASJ AF: 0.822

Gnomad4 EAS AF: 0.916

Gnomad4 SAS AF: 0.811

Gnomad4 FIN AF: 0.673

Gnomad4 NFE AF: 0.696

Gnomad4 OTH AF: 0.785

Alfa AF: 0.716 Hom.: 78795

Bravo AF: 0.780

Asia WGS AF: 0.829 AC: 2884 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.82
DANN	Benign	0.60

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: rs8045689; hg19: chr16-28988269;