Genetic Variant NM_022827.4:c.296+14C>T (chr17-50548467-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_022827.4(SPATA20):c.296+14C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.391 in 1,613,004 control chromosomes in the GnomAD database, including 132,672 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 ( 20518 hom., cov: 32)

Exomes 𝑓: 0.38 ( 112154 hom. )

Consequence

SPATA20
NM_022827.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.377

Publications

32 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 (BayesDel_noAF=-0.81).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.77 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_022827.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
SPATA20	NM_022827.4	MANE Select	c.296+14C>T	intron	N/A	NP_073738.2
SPATA20	NM_001258372.2		c.248+14C>T	intron	N/A	NP_001245301.1
SPATA20	NM_001258373.2		c.116+14C>T	intron	N/A	NP_001245302.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
SPATA20	ENST00000006658.11	TSL:1 MANE Select	c.296+14C>T	intron	N/A	ENSP00000006658.6
SPATA20	ENST00000356488.8	TSL:1	c.248+14C>T	intron	N/A	ENSP00000348878.4
SPATA20	ENST00000503127.5	TSL:1	n.*219+14C>T	intron	N/A	ENSP00000426228.1

Frequencies

GnomAD3 genomes

AF:

0.482

AC:

73308

AN:

151948

Hom.:

20468

Cov.:

show subpopulations

Gnomad AFR

AF:

0.777

Gnomad AMI

AF:

0.532

Gnomad AMR

AF:

0.455

Gnomad ASJ

AF:

0.475

Gnomad EAS

AF:

0.124

Gnomad SAS

AF:

0.235

Gnomad FIN

AF:

0.348

Gnomad MID

AF:

0.348

Gnomad NFE

AF:

0.376

Gnomad OTH

AF:

0.456

GnomAD2 exomes

AF:

0.385

AC:

95925

AN:

249324

AF XY:

0.370

show subpopulations

Gnomad AFR exome

AF:

0.784

Gnomad AMR exome

AF:

0.453

Gnomad ASJ exome

AF:

0.490

Gnomad EAS exome

AF:

0.116

Gnomad FIN exome

AF:

0.359

Gnomad NFE exome

AF:

0.386

Gnomad OTH exome

AF:

0.391

GnomAD4 exome

AF:

0.381

AC:

556726

AN:

1460938

Hom.:

112154

Cov.:

AF XY:

0.375

AC XY:

272749

AN XY:

726730

show subpopulations

African (AFR)

AF:

0.796

AC:

26636

AN:

33474

American (AMR)

AF:

0.449

AC:

20031

AN:

44588

Ashkenazi Jewish (ASJ)

AF:

0.484

AC:

12630

AN:

26084

East Asian (EAS)

AF:

0.113

AC:

4487

AN:

39696

South Asian (SAS)

AF:

0.242

AC:

20885

AN:

86216

European-Finnish (FIN)

AF:

0.365

AC:

19449

AN:

53288

Middle Eastern (MID)

AF:

0.405

AC:

2334

AN:

5760

European-Non Finnish (NFE)

AF:

0.383

AC:

426145

AN:

1111474

Other (OTH)

AF:

0.400

AC:

24129

AN:

60358

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.476

Heterozygous variant carriers

19573

39146

58719

78292

97865

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

13406

26812

40218

53624

67030

<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:

0.483

AC:

73419

AN:

152066

Hom.:

20518

Cov.:

AF XY:

0.475

AC XY:

35319

AN XY:

74316

show subpopulations

African (AFR)

AF:

0.777

AC:

32223

AN:

41476

American (AMR)

AF:

0.456

AC:

6964

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.475

AC:

1647

AN:

3468

East Asian (EAS)

AF:

0.125

AC:

645

AN:

5170

South Asian (SAS)

AF:

0.234

AC:

1128

AN:

4822

European-Finnish (FIN)

AF:

0.348

AC:

3681

AN:

10586

Middle Eastern (MID)

AF:

0.347

AC:

102

AN:

294

European-Non Finnish (NFE)

AF:

0.376

AC:

25567

AN:

67940

Other (OTH)

AF:

0.463

AC:

977

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1687

3373

5060

6746

8433

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

598

1196

1794

2392

2990

<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:

0.410

Hom.:

45146

Bravo

AF:

0.509

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

3.5

(source)

DANN

Benign

0.43

PhyloP100

0.38

PromoterAI

0.029

Neutral

(source)

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over