dbSNP rs7140: SPNS1:c.*137C>A (chr16-28984436-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_032038.3(SPNS1):c.*137C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.726 in 854,248 control chromosomes in the GnomAD database, including 229,198 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 ( 45475 hom., cov: 34)

Exomes 𝑓: 0.72 ( 183723 hom. )

Consequence

SPNS1
NM_032038.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.46

Publications

29 publications found

Variant links:

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 links:

ENSG00000261067 (HGNC:):

ENSG00000261067 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=7.219226E-7).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.906 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SPNS1	NM_032038.3 link	c.*137C>A		3_prime_UTR_variant	Exon 12 of 12	ENST00000311008.16	NP_114427.1	Q9H2V7-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SPNS1	ENST00000311008.16 link	c.*137C>A		3_prime_UTR_variant	Exon 12 of 12	1	NM_032038.3	ENSP00000309945.11		Q9H2V7-1

Frequencies

GnomAD3 genomes

AF:

0.765

AC:

116330

AN:

152056

Hom.:

45424

Cov.:

show subpopulations

Gnomad AFR

AF:

0.913

Gnomad AMI

AF:

0.760

Gnomad AMR

AF:

0.655

Gnomad ASJ

AF:

0.822

Gnomad EAS

AF:

0.915

Gnomad SAS

AF:

0.810

Gnomad FIN

AF:

0.673

Gnomad MID

AF:

0.854

Gnomad NFE

AF:

0.696

Gnomad OTH

AF:

0.779

GnomAD2 exomes

AF:

0.729

AC:

101296

AN:

138880

AF XY:

0.739

show subpopulations

Gnomad AFR exome

AF:

0.922

Gnomad AMR exome

AF:

0.560

Gnomad ASJ exome

AF:

0.817

Gnomad EAS exome

AF:

0.927

Gnomad FIN exome

AF:

0.670

Gnomad NFE exome

AF:

0.702

Gnomad OTH exome

AF:

0.742

GnomAD4 exome

AF:

0.717

AC:

503712

AN:

702074

Hom.:

183723

Cov.:

AF XY:

0.722

AC XY:

267345

AN XY:

370072

show subpopulations

African (AFR)

AF:

0.920

AC:

17069

AN:

18550

American (AMR)

AF:

0.559

AC:

19520

AN:

34898

Ashkenazi Jewish (ASJ)

AF:

0.816

AC:

17064

AN:

20906

East Asian (EAS)

AF:

0.920

AC:

30156

AN:

32784

South Asian (SAS)

AF:

0.807

AC:

52683

AN:

65268

European-Finnish (FIN)

AF:

0.665

AC:

22617

AN:

34030

Middle Eastern (MID)

AF:

0.866

AC:

3784

AN:

4372

European-Non Finnish (NFE)

AF:

0.690

AC:

314217

AN:

455596

Other (OTH)

AF:

0.746

AC:

26602

AN:

35670

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.514

Heterozygous variant carriers

8159

16318

24476

32635

40794

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

4188

8376

12564

16752

20940

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.765

AC:

116427

AN:

152174

Hom.:

45475

Cov.:

AF XY:

0.764

AC XY:

56851

AN XY:

74390

show subpopulations

African (AFR)

AF:

0.913

AC:

37952

AN:

41554

American (AMR)

AF:

0.654

AC:

10000

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.822

AC:

2853

AN:

3470

East Asian (EAS)

AF:

0.915

AC:

4719

AN:

5156

South Asian (SAS)

AF:

0.810

AC:

3903

AN:

4818

European-Finnish (FIN)

AF:

0.673

AC:

7127

AN:

10594

Middle Eastern (MID)

AF:

0.861

AC:

253

AN:

294

European-Non Finnish (NFE)

AF:

0.696

AC:

47279

AN:

67976

Other (OTH)

AF:

0.780

AC:

1648

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1382

2764

4146

5528

6910

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

852

1704

2556

3408

4260

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.724

Hom.:

79125

Bravo

AF:

0.771

TwinsUK

AF:

0.698

AC:

2587

ALSPAC

AF:

0.691

AC:

2665

ExAC

AF:

0.644

AC:

44792

Asia WGS

AF:

0.825

AC:

2872

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.11

BayesDel_addAF

Benign

-0.69

BayesDel_noAF

Benign

-0.62

CADD

Benign

6.5

(source)

DANN

Benign

0.90

DEOGEN2

Benign

0.0052

FATHMM_MKL

Benign

0.0014

LIST_S2

Benign

0.14

MetaRNN

Benign

7.2e-7

PhyloP100

-1.5

PROVEAN

Benign

-0.17

Sift

Pathogenic

0.0

Sift4G

Benign

1.0

GERP RS

0.77

PromoterAI

-0.0048

Neutral

(source)

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over