16-28976948-C-T

Variant names:

• chr16-28976948-C-T
• rs8045689
• NM_032038.3:c.308-960C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 39 publications found

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]

ENSG00000260367 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032038.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPNS1	NM_032038.3	MANE Select	c.308-960C>T		intron	N/A	NP_114427.1	Q9H2V7-1
	SPNS1	NM_001142448.2		c.308-960C>T		intron	N/A	NP_001135920.1	Q9H2V7-1
	SPNS1	NM_001142451.2		c.308-960C>T		intron	N/A	NP_001135923.1	Q9H2V7-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPNS1	ENST00000311008.16	TSL:1 MANE Select	c.308-960C>T		intron	N/A	ENSP00000309945.11	Q9H2V7-1
	SPNS1	ENST00000565975.5	TSL:1	c.443-960C>T		intron	N/A	ENSP00000454360.1	H3BMF4
	SPNS1	ENST00000334536.12	TSL:1	c.308-960C>T		intron	N/A	ENSP00000335494.8	Q9H2V7-2

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

African (AFR) AF: 0.943 AC: 39180 AN: 41544

American (AMR) AF: 0.659 AC: 10057 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.822 AC: 2855 AN: 3472

East Asian (EAS) AF: 0.916 AC: 4753 AN: 5190

South Asian (SAS) AF: 0.811 AC: 3919 AN: 4832

European-Finnish (FIN) AF: 0.673 AC: 7105 AN: 10564

Middle Eastern (MID) AF: 0.864 AC: 254 AN: 294

European-Non Finnish (NFE) AF: 0.696 AC: 47299 AN: 67996

Other (OTH) AF: 0.785 AC: 1662 AN: 2116

Alfa AF: 0.727 Hom.: 126362

Bravo AF: 0.780

Asia WGS AF: 0.829 AC: 2884 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.82
DANN	Benign	0.60
PhyloP100		-0.71
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs8045689; hg19: chr16-28988269;