Genetic Variant NM_022827.4:c.310C>G (chr17-50548567-C-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_022827.4(SPATA20):c.310C>G(p.Gln104Glu) variant causes a missense change. The variant allele was found at a frequency of 0.359 in 1,611,484 control chromosomes in the GnomAD database, including 110,899 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.42 ( 15029 hom., cov: 32)

Exomes 𝑓: 0.35 ( 95870 hom. )

Consequence

SPATA20
NM_022827.4 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.36

Publications

58 publications found

Variant links:

Genes affected

SPATA20 (HGNC:26125): (spermatogenesis associated 20) Predicted to be involved in carbohydrate metabolic process; cell differentiation; and spermatogenesis. Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Apr 2022]

SPATA20 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=8.233564E-6).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.637 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein
SPATA20	NM_022827.4 link	c.310C>G	p.Gln104Glu	missense_variant	Exon 4 of 17	ENST00000006658.11	NP_073738.2
SPATA20	NM_001258372.2 link	c.262C>G	p.Gln88Glu	missense_variant	Exon 3 of 16		NP_001245301.1
SPATA20	NM_001258373.2 link	c.130C>G	p.Gln44Glu	missense_variant	Exon 4 of 17		NP_001245302.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SPATA20	ENST00000006658.11 link	c.310C>G	p.Gln104Glu	missense_variant	Exon 4 of 17	1	NM_022827.4	ENSP00000006658.6

Frequencies

GnomAD3 genomes

AF:

0.418

AC:

63497

AN:

151896

Hom.:

15013

Cov.:

show subpopulations

Gnomad AFR

AF:

0.644

Gnomad AMI

AF:

0.532

Gnomad AMR

AF:

0.323

Gnomad ASJ

AF:

0.425

Gnomad EAS

AF:

0.0734

Gnomad SAS

AF:

0.197

Gnomad FIN

AF:

0.323

Gnomad MID

AF:

0.323

Gnomad NFE

AF:

0.358

Gnomad OTH

AF:

0.396

GnomAD2 exomes

AF:

0.321

AC:

79293

AN:

247362

AF XY:

0.314

show subpopulations

Gnomad AFR exome

AF:

0.644

Gnomad AMR exome

AF:

0.239

Gnomad ASJ exome

AF:

0.439

Gnomad EAS exome

AF:

0.0676

Gnomad FIN exome

AF:

0.327

Gnomad NFE exome

AF:

0.362

Gnomad OTH exome

AF:

0.335

GnomAD4 exome

AF:

0.352

AC:

514334

AN:

1459470

Hom.:

95870

Cov.:

AF XY:

0.347

AC XY:

252161

AN XY:

725904

show subpopulations

African (AFR)

AF:

0.656

AC:

21914

AN:

33406

American (AMR)

AF:

0.248

AC:

11040

AN:

44482

Ashkenazi Jewish (ASJ)

AF:

0.434

AC:

11319

AN:

26082

East Asian (EAS)

AF:

0.0763

AC:

3025

AN:

39668

South Asian (SAS)

AF:

0.205

AC:

17679

AN:

86114

European-Finnish (FIN)

AF:

0.332

AC:

17602

AN:

53070

Middle Eastern (MID)

AF:

0.362

AC:

2088

AN:

5760

European-Non Finnish (NFE)

AF:

0.367

AC:

407872

AN:

1110582

Other (OTH)

AF:

0.361

AC:

21795

AN:

60306

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.453

Heterozygous variant carriers

18203

36407

54610

72814

91017

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

12876

25752

38628

51504

64380

<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:

0.418

AC:

63547

AN:

152014

Hom.:

15029

Cov.:

AF XY:

0.410

AC XY:

30472

AN XY:

74294

show subpopulations

African (AFR)

AF:

0.643

AC:

26658

AN:

41446

American (AMR)

AF:

0.322

AC:

4924

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.425

AC:

1474

AN:

3468

East Asian (EAS)

AF:

0.0735

AC:

381

AN:

5182

South Asian (SAS)

AF:

0.197

AC:

948

AN:

4822

European-Finnish (FIN)

AF:

0.323

AC:

3420

AN:

10586

Middle Eastern (MID)

AF:

0.327

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.358

AC:

24336

AN:

67922

Other (OTH)

AF:

0.391

AC:

826

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1700

3400

5100

6800

8500

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

548

1096

1644

2192

2740

<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:

0.382

Hom.:

3587

Bravo

AF:

0.431

TwinsUK

AF:

0.361

AC:

1339

ALSPAC

AF:

0.364

AC:

1404

ESP6500AA

AF:

0.635

AC:

2797

ESP6500EA

AF:

0.361

AC:

3108

ExAC

AF:

0.329

AC:

39911

Asia WGS

AF:

0.175

AC:

610

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.077

BayesDel_addAF

Benign

-0.58

BayesDel_noAF

Benign

-0.46

CADD

Benign

(source)

DANN

Benign

0.89

DEOGEN2

Benign

0.0

.;.;T;T

Eigen

Benign

-0.49

Eigen_PC

Benign

-0.20

FATHMM_MKL

Pathogenic

0.99

LIST_S2

Benign

0.81

T;T;T;T

MetaRNN

Benign

0.0000082

T;T;T;T

MetaSVM

Benign

-0.96

MutationAssessor

Benign

0.0

.;.;N;.

PhyloP100

4.4

PrimateAI

Benign

0.46

PROVEAN

Benign

0.0

.;N;N;.

REVEL

Benign

0.0

Sift

Pathogenic

0.0

.;T;T;.

Sift4G

Benign

1.0

T;T;T;T

Vest4

0.18

ClinPred

0.024

GERP RS

4.6

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Varity_R

0.26

gMVP

0.28

Mutation Taster

=95/5

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