rs8045689

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr16-28976948-C-G
• chr16-28976948-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_032038.3(SPNS1):​c.308-960C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).

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>G		intron	N/A	NP_114427.1	Q9H2V7-1
	SPNS1	NM_001142448.2		c.308-960C>G		intron	N/A	NP_001135920.1	Q9H2V7-1
	SPNS1	NM_001142451.2		c.308-960C>G		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>G		intron	N/A	ENSP00000309945.11	Q9H2V7-1
	SPNS1	ENST00000565975.5	TSL:1	c.443-960C>G		intron	N/A	ENSP00000454360.1	H3BMF4
	SPNS1	ENST00000334536.12	TSL:1	c.308-960C>G		intron	N/A	ENSP00000335494.8	Q9H2V7-2

Frequencies

GnomAD3 genomes Cov.: 33

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

GnomAD4 genome Cov.: 33

Alfa AF: 0.00 Hom.: 126362

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.42
DANN	Benign	0.48
PhyloP100		-0.71

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;