Genetic Variant NM_003124.5:c.112G>A (chr2-72887544-G-A) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 3P and 13B. PM1PP2BP4_StrongBP6BS1BS2

The NM_003124.5(SPR):c.112G>A(p.Val38Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00591 in 1,466,384 control chromosomes in the GnomAD database, including 37 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

Frequency

Genomes: 𝑓 0.0051 ( 4 hom., cov: 33)

Exomes 𝑓: 0.0060 ( 33 hom. )

Consequence

SPR
NM_003124.5 missense

Scores

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:1B:8

Conservation

PhyloP100: 1.35

Publications

7 publications found

Variant links:

Genes affected

SPR (HGNC:11257): (sepiapterin reductase) This gene encodes an aldo-keto reductase that catalyzes the NADPH-dependent reduction of pteridine derivatives and is important in the biosynthesis of tetrahydrobiopterin (BH4). Mutations in this gene result in DOPA-responsive dystonia due to sepiaterin reductase deficiency. A pseudogene has been identified on chromosome 1. [provided by RefSeq, Jul 2008]

SPR Gene-Disease associations (from GenCC):

dopa-responsive dystonia due to sepiapterin reductase deficiency
Inheritance: AR, AD Classification: DEFINITIVE, STRONG, MODERATE, SUPPORTIVE Submitted by: Ambry Genetics, G2P, PanelApp Australia, Genomics England PanelApp, ClinGen, Orphanet
BH4-deficient hyperphenylalaninemia A
Inheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)

SPR links:

ENSG00000309317 (HGNC:):

ENSG00000309317 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

PM1

In a chain Sepiapterin reductase (size 260) in uniprot entity SPRE_HUMAN there are 9 pathogenic changes around while only 2 benign (82%) in NM_003124.5

PP2

Missense variant in the gene, where a lot of missense mutations are associated with disease in ClinVar. The gene has 6 curated pathogenic missense variants (we use a threshold of 10). The gene has 1 curated benign missense variants. Gene score misZ: 0.7325 (below the threshold of 3.09). Trascript score misZ: -0.70614 (below the threshold of 3.09). GenCC associations: The gene is linked to dopa-responsive dystonia due to sepiapterin reductase deficiency, BH4-deficient hyperphenylalaninemia A.

BP4

Computational evidence support a benign effect (MetaRNN=0.010404646).

BP6

Variant 2-72887544-G-A is Benign according to our data. Variant chr2-72887544-G-A is described in ClinVar as Conflicting_classifications_of_pathogenicity. ClinVar VariationId is 239509.

BS1

Variant frequency is greater than expected in population amr. GnomAd4 allele frequency = 0.00511 (778/152188) while in subpopulation AMR AF = 0.00941 (144/15296). AF 95% confidence interval is 0.00816. There are 4 homozygotes in GnomAd4. There are 369 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.

BS2

High Homozygotes in GnomAd4 at 4 AD,AR gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003124.5. 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
	SPR	NM_003124.5	MANE Select	c.112G>A	p.Val38Ile	missense	Exon 1 of 3	NP_003115.1	P35270

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
SPR	ENST00000234454.6	TSL:1 MANE Select	c.112G>A	p.Val38Ile	missense	Exon 1 of 3	ENSP00000234454.5	P35270
SPR	ENST00000871611.1		c.112G>A	p.Val38Ile	missense	Exon 1 of 3	ENSP00000541670.1
SPR	ENST00000871609.1		c.112G>A	p.Val38Ile	missense	Exon 1 of 3	ENSP00000541668.1

Frequencies

GnomAD3 genomes

AF:

0.00512

AC:

778

AN:

152080

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00145

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00943

Gnomad ASJ

AF:

0.00202

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000414

Gnomad FIN

AF:

0.00416

Gnomad MID

AF:

0.00318

Gnomad NFE

AF:

0.00759

Gnomad OTH

AF:

0.00191

GnomAD2 exomes

AF:

0.00387

AC:

283

AN:

73058

AF XY:

0.00347

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00331

Gnomad ASJ exome

AF:

0.00289

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00378

Gnomad NFE exome

AF:

0.00689

Gnomad OTH exome

AF:

0.00438

GnomAD4 exome

AF:

0.00601

AC:

7894

AN:

1314196

Hom.:

Cov.:

AF XY:

0.00587

AC XY:

3800

AN XY:

647536

show subpopulations

African (AFR)

AF:

0.00113

AC:

AN:

26610

American (AMR)

AF:

0.00368

AC:

AN:

24728

Ashkenazi Jewish (ASJ)

AF:

0.00311

AC:

AN:

22526

East Asian (EAS)

AF:

0.00

AC:

AN:

28426

South Asian (SAS)

AF:

0.000538

AC:

AN:

70614

European-Finnish (FIN)

AF:

0.00350

AC:

119

AN:

34028

Middle Eastern (MID)

AF:

0.00122

AC:

AN:

4110

European-Non Finnish (NFE)

AF:

0.00695

AC:

7292

AN:

1048708

Other (OTH)

AF:

0.00457

AC:

249

AN:

54446

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.479

Heterozygous variant carriers

520

1040

1559

2079

2599

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

268

536

804

1072

1340

<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:

0.00511

AC:

778

AN:

152188

Hom.:

Cov.:

AF XY:

0.00496

AC XY:

369

AN XY:

74418

show subpopulations

African (AFR)

AF:

0.00144

AC:

AN:

41560

American (AMR)

AF:

0.00941

AC:

144

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.00202

AC:

AN:

3466

East Asian (EAS)

AF:

0.00

AC:

AN:

5172

South Asian (SAS)

AF:

0.000414

AC:

AN:

4832

European-Finnish (FIN)

AF:

0.00416

AC:

AN:

10574

Middle Eastern (MID)

AF:

0.00342

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.00759

AC:

516

AN:

67972

Other (OTH)

AF:

0.00189

AC:

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.495

Heterozygous variant carriers

130

174

217

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

<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:

0.00535

Hom.:

Bravo

AF:

0.00460

TwinsUK

AF:

0.00405

AC:

ALSPAC

AF:

0.00623

AC:

ESP6500AA

AF:

0.00158

AC:

ESP6500EA

AF:

0.00491

AC:

ExAC

AF:

0.00171

AC:

169

ClinVar

ClinVar submissions

Significance:Conflicting classifications of pathogenicity

Revision:criteria provided, conflicting classifications

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (4)

Dopa-responsive dystonia due to sepiapterin reductase deficiency (2)

Dystonic disorder (1)

not specified (1)

SPR-related disorder (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.12

BayesDel_addAF

Benign

-0.35

BayesDel_noAF

Benign

-0.27

CADD

Benign

(source)

DANN

Uncertain

1.0

DEOGEN2

Benign

0.31

Eigen

Benign

-0.39

Eigen_PC

Benign

-0.30

FATHMM_MKL

Benign

0.68

LIST_S2

Uncertain

0.88

MetaRNN

Benign

0.010

MetaSVM

Benign

-0.34

MutationAssessor

Benign

1.2

PhyloP100

1.3

PrimateAI

Uncertain

0.74

PROVEAN

Benign

-0.33

REVEL

Benign

0.20

Sift

Uncertain

0.026

Sift4G

Benign

0.19

Polyphen

0.051

Vest4

0.12

MVP

0.84

MPC

0.42

ClinPred

0.029

GERP RS

3.2

PromoterAI

-0.0082

Neutral

(source)

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.6

Varity_R

0.19

gMVP

0.24

Mutation Taster

=97/3

polymorphism

(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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over