Genetic Variant SVOP:c.898-49G>A (chr12-108937386-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_018711.5(SVOP):c.898-49G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.414 in 1,574,166 control chromosomes in the GnomAD database, including 138,607 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 0.48 ( 18339 hom., cov: 31)

Exomes 𝑓: 0.41 ( 120268 hom. )

Consequence

SVOP
NM_018711.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.456

Publications

11 publications found

Variant links:

Genes affected

SVOP (HGNC:25417): (SV2 related protein) Predicted to enable transmembrane transporter activity. Predicted to be involved in transmembrane transport. Predicted to be located in synaptic vesicle. [provided by Alliance of Genome Resources, Apr 2022]

SVOP links:

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ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.625 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SVOP	NM_018711.5 link	c.898-49G>A		intron_variant	Intron 9 of 15	ENST00000610966.5	NP_061181.1	Q8N4V2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SVOP	ENST00000610966.5 link	c.898-49G>A		intron_variant	Intron 9 of 15	1	NM_018711.5	ENSP00000479104.1		Q8N4V2
SVOP	ENST00000551211.1 link	n.63-49G>A		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes

AF:

0.477

AC:

72438

AN:

151788

Hom.:

18289

Cov.:

show subpopulations

Gnomad AFR

AF:

0.631

Gnomad AMI

AF:

0.410

Gnomad AMR

AF:

0.558

Gnomad ASJ

AF:

0.384

Gnomad EAS

AF:

0.514

Gnomad SAS

AF:

0.369

Gnomad FIN

AF:

0.428

Gnomad MID

AF:

0.471

Gnomad NFE

AF:

0.383

Gnomad OTH

AF:

0.485

GnomAD2 exomes

AF:

0.448

AC:

111624

AN:

248996

AF XY:

0.435

show subpopulations

Gnomad AFR exome

AF:

0.635

Gnomad AMR exome

AF:

0.631

Gnomad ASJ exome

AF:

0.387

Gnomad EAS exome

AF:

0.517

Gnomad FIN exome

AF:

0.418

Gnomad NFE exome

AF:

0.386

Gnomad OTH exome

AF:

0.439

GnomAD4 exome

AF:

0.407

AC:

578469

AN:

1422260

Hom.:

120268

Cov.:

AF XY:

0.404

AC XY:

286880

AN XY:

709864

show subpopulations

African (AFR)

AF:

0.644

AC:

21109

AN:

32766

American (AMR)

AF:

0.623

AC:

27793

AN:

44636

Ashkenazi Jewish (ASJ)

AF:

0.383

AC:

9896

AN:

25870

East Asian (EAS)

AF:

0.526

AC:

20796

AN:

39510

South Asian (SAS)

AF:

0.384

AC:

32793

AN:

85402

European-Finnish (FIN)

AF:

0.414

AC:

22063

AN:

53272

Middle Eastern (MID)

AF:

0.462

AC:

2646

AN:

5730

European-Non Finnish (NFE)

AF:

0.387

AC:

416685

AN:

1076032

Other (OTH)

AF:

0.418

AC:

24688

AN:

59042

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

17080

34160

51241

68321

85401

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

13138

26276

39414

52552

65690

<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:

0.478

AC:

72556

AN:

151906

Hom.:

18339

Cov.:

AF XY:

0.479

AC XY:

35557

AN XY:

74216

show subpopulations

African (AFR)

AF:

0.632

AC:

26179

AN:

41434

American (AMR)

AF:

0.558

AC:

8522

AN:

15268

Ashkenazi Jewish (ASJ)

AF:

0.384

AC:

1333

AN:

3470

East Asian (EAS)

AF:

0.515

AC:

2658

AN:

5160

South Asian (SAS)

AF:

0.370

AC:

1781

AN:

4816

European-Finnish (FIN)

AF:

0.428

AC:

4503

AN:

10510

Middle Eastern (MID)

AF:

0.469

AC:

137

AN:

292

European-Non Finnish (NFE)

AF:

0.383

AC:

26044

AN:

67938

Other (OTH)

AF:

0.487

AC:

1026

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1850

3700

5550

7400

9250

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

634

1268

1902

2536

3170

<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:

0.417

Hom.:

58296

Bravo

AF:

0.498

Asia WGS

AF:

0.480

AC:

1669

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.043

(source)

DANN

Benign

0.43

PhyloP100

-0.46

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