dbSNP rs28381989: SPATA4:p.Arg279LysfsTer4 (chr4-176184858-TTCTC-T) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_144644.4(SPATA4):c.836_839delGAGA(p.Arg279LysfsTer4) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.11 in 1,596,384 control chromosomes in the GnomAD database, including 11,259 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.085 ( 776 hom., cov: 31)

Exomes 𝑓: 0.11 ( 10483 hom. )

Consequence

SPATA4
NM_144644.4 frameshift

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.11

Publications

11 publications found

Variant links:

Genes affected

SPATA4 (HGNC:17333): (spermatogenesis associated 4) Predicted to enable microtubule binding activity. Predicted to be involved in regulation of cytoskeleton organization. Predicted to be located in cytoplasm. Predicted to be active in axoneme. [provided by Alliance of Genome Resources, Apr 2022]

SPATA4 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.125 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_144644.4. 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
	SPATA4	NM_144644.4	MANE Select	c.836_839delGAGA	p.Arg279LysfsTer4	frameshift	Exon 6 of 6	NP_653245.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPATA4	ENST00000280191.7	TSL:1 MANE Select	c.836_839delGAGA	p.Arg279LysfsTer4	frameshift	Exon 6 of 6	ENSP00000280191.2	Q8NEY3
	SPATA4	ENST00000515234.1	TSL:1	c.317_320delGAGA	p.Arg106LysfsTer4	frameshift	Exon 5 of 5	ENSP00000422290.1	G5E9Y6

Frequencies

GnomAD3 genomes

AF:

0.0848

AC:

12891

AN:

152076

Hom.:

776

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0221

Gnomad AMI

AF:

0.0989

Gnomad AMR

AF:

0.0554

Gnomad ASJ

AF:

0.107

Gnomad EAS

AF:

0.00115

Gnomad SAS

AF:

0.0315

Gnomad FIN

AF:

0.160

Gnomad MID

AF:

0.0414

Gnomad NFE

AF:

0.127

Gnomad OTH

AF:

0.0813

GnomAD2 exomes

AF:

0.0866

AC:

20676

AN:

238762

AF XY:

0.0870

show subpopulations

Gnomad AFR exome

AF:

0.0176

Gnomad AMR exome

AF:

0.0345

Gnomad ASJ exome

AF:

0.103

Gnomad EAS exome

AF:

0.000171

Gnomad FIN exome

AF:

0.160

Gnomad NFE exome

AF:

0.124

Gnomad OTH exome

AF:

0.0880

GnomAD4 exome

AF:

0.113

AC:

162521

AN:

1444188

Hom.:

10483

AF XY:

0.111

AC XY:

79613

AN XY:

718350

show subpopulations

African (AFR)

AF:

0.0150

AC:

492

AN:

32884

American (AMR)

AF:

0.0368

AC:

1561

AN:

42426

Ashkenazi Jewish (ASJ)

AF:

0.102

AC:

2626

AN:

25792

East Asian (EAS)

AF:

0.000180

AC:

AN:

38966

South Asian (SAS)

AF:

0.0331

AC:

2773

AN:

83858

European-Finnish (FIN)

AF:

0.158

AC:

8408

AN:

53052

Middle Eastern (MID)

AF:

0.0325

AC:

186

AN:

5726

European-Non Finnish (NFE)

AF:

0.128

AC:

140671

AN:

1101802

Other (OTH)

AF:

0.0971

AC:

5797

AN:

59682

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.420

Heterozygous variant carriers

6537

13074

19611

26148

32685

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

4886

9772

14658

19544

24430

<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:

0.0847

AC:

12886

AN:

152196

Hom.:

776

Cov.:

AF XY:

0.0825

AC XY:

6139

AN XY:

74402

show subpopulations

African (AFR)

AF:

0.0220

AC:

916

AN:

41564

American (AMR)

AF:

0.0552

AC:

844

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.107

AC:

372

AN:

3470

East Asian (EAS)

AF:

0.00116

AC:

AN:

5186

South Asian (SAS)

AF:

0.0315

AC:

152

AN:

4820

European-Finnish (FIN)

AF:

0.160

AC:

1689

AN:

10574

Middle Eastern (MID)

AF:

0.0374

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.127

AC:

8636

AN:

67978

Other (OTH)

AF:

0.0804

AC:

170

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.494

Heterozygous variant carriers

598

1196

1795

2393

2991

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

156

312

468

624

780

<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:

0.108

Hom.:

180

Bravo

AF:

0.0741

Asia WGS

AF:

0.0160

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

2.1

Mutation Taster

=134/66

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