Genetic Variant 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:

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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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SPATA4	NM_144644.4 link	c.836_839delGAGA	p.Arg279LysfsTer4	frameshift_variant	Exon 6 of 6	ENST00000280191.7	NP_653245.2	Q8NEY3
SPATA4	XM_047449608.1 link	c.317_320delGAGA	p.Arg106LysfsTer4	frameshift_variant	Exon 6 of 6		XP_047305564.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SPATA4	ENST00000280191.7 link	c.836_839delGAGA	p.Arg279LysfsTer4	frameshift_variant	Exon 6 of 6	1	NM_144644.4	ENSP00000280191.2		Q8NEY3
SPATA4	ENST00000515234.1 link	c.317_320delGAGA	p.Arg106LysfsTer4	frameshift_variant	Exon 5 of 5	1		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

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

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 v4.3

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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chr4-176184858-TTCTC-T

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