Variant chr5-139396890-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_194296.2(SPATA24):c.528G>A(p.Glu176Glu) variant causes a synonymous change. The variant allele was found at a frequency of 0.624 in 1,551,496 control chromosomes in the GnomAD database, including 314,613 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 0.50 ( 22364 hom., cov: 32)

Exomes 𝑓: 0.64 ( 292249 hom. )

Consequence

SPATA24
NM_194296.2 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.90

Variant links:

Genes affected

SPATA24 (HGNC:27322): (spermatogenesis associated 24) Predicted to enable DNA binding activity and identical protein binding activity. Predicted to be involved in cell differentiation and spermatogenesis. Located in cytosol and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

SPATA24 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=9.923242E-6).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.66 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SPATA24	NM_194296.2 linkuse as main transcript	c.528G>A	p.Glu176Glu	synonymous_variant	6/6	ENST00000450845.7	NP_919272.1	Q86W54-1
SPATA24	XM_005271916.5 linkuse as main transcript	c.554G>A	p.Arg185Lys	missense_variant	6/6		XP_005271973.1
SPATA24	XM_011543252.3 linkuse as main transcript	c.437G>A	p.Arg146Lys	missense_variant	6/6		XP_011541554.1
SPATA24	XM_011543253.3 linkuse as main transcript	c.437G>A	p.Arg146Lys	missense_variant	6/6		XP_011541555.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
SPATA24	ENST00000450845.7 linkuse as main transcript	c.528G>A	p.Glu176Glu	synonymous_variant	6/6	1	NM_194296.2	ENSP00000414920.2	Q86W54-1
SPATA24	ENST00000302091.9 linkuse as main transcript	c.554G>A	p.Arg185Lys	missense_variant	6/6	2		ENSP00000302917.5	Q8N799
SPATA24	ENST00000514983.5 linkuse as main transcript	c.413G>A	p.Arg138Lys	missense_variant	5/5	5		ENSP00000423424.1	H0Y992
SPATA24	ENST00000512761.5 linkuse as main transcript	c.372G>A	p.Glu124Glu	synonymous_variant	5/5	5		ENSP00000426748.1	H0YAD3

Frequencies

GnomAD3 genomes

AF:

0.497

AC:

75531

AN:

151992

Hom.:

22372

Cov.:

show subpopulations

Gnomad AFR

AF:

0.170

Gnomad AMI

AF:

0.592

Gnomad AMR

AF:

0.539

Gnomad ASJ

AF:

0.535

Gnomad EAS

AF:

0.306

Gnomad SAS

AF:

0.545

Gnomad FIN

AF:

0.684

Gnomad MID

AF:

0.522

Gnomad NFE

AF:

0.665

Gnomad OTH

AF:

0.510

GnomAD3 exomes

AF:

0.584

AC:

91392

AN:

156548

Hom.:

28235

AF XY:

0.586

AC XY:

48659

AN XY:

82970

show subpopulations

Gnomad AFR exome

AF:

0.158

Gnomad AMR exome

AF:

0.624

Gnomad ASJ exome

AF:

0.537

Gnomad EAS exome

AF:

0.297

Gnomad SAS exome

AF:

0.553

Gnomad FIN exome

AF:

0.700

Gnomad NFE exome

AF:

0.660

Gnomad OTH exome

AF:

0.585

GnomAD4 exome

AF:

0.638

AC:

892645

AN:

1399384

Hom.:

292249

Cov.:

AF XY:

0.637

AC XY:

439555

AN XY:

690200

show subpopulations

Gnomad4 AFR exome

AF:

0.161

Gnomad4 AMR exome

AF:

0.613

Gnomad4 ASJ exome

AF:

0.530

Gnomad4 EAS exome

AF:

0.342

Gnomad4 SAS exome

AF:

0.553

Gnomad4 FIN exome

AF:

0.690

Gnomad4 NFE exome

AF:

0.672

Gnomad4 OTH exome

AF:

0.581

GnomAD4 genome

AF:

0.496

AC:

75523

AN:

152112

Hom.:

22364

Cov.:

AF XY:

0.496

AC XY:

36854

AN XY:

74362

show subpopulations

Gnomad4 AFR

AF:

0.169

Gnomad4 AMR

AF:

0.539

Gnomad4 ASJ

AF:

0.535

Gnomad4 EAS

AF:

0.306

Gnomad4 SAS

AF:

0.546

Gnomad4 FIN

AF:

0.684

Gnomad4 NFE

AF:

0.665

Gnomad4 OTH

AF:

0.506

Alfa

AF:

0.616

Hom.:

47876

Bravo

AF:

0.474

TwinsUK

AF:

0.655

AC:

2428

ALSPAC

AF:

0.667

AC:

2569

ESP6500AA

AF:

0.169

AC:

234

ESP6500EA

AF:

0.650

AC:

2067

ExAC

AF:

0.526

AC:

12915

Asia WGS

AF:

0.398

AC:

1383

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.22

BayesDel_noAF

Uncertain

0.060

CADD

Benign

9.3

DANN

Uncertain

0.99

DEOGEN2

Benign

0.0040

Eigen

Uncertain

0.64

Eigen_PC

Uncertain

0.66

FATHMM_MKL

Uncertain

0.77

LIST_S2

Benign

0.35

MetaRNN

Benign

0.0000099

MetaSVM

Benign

-0.91

PROVEAN

Benign

0.32

REVEL

Benign

0.21

Sift

Benign

0.14

Polyphen

1.0

ClinPred

0.034

GERP RS

5.7

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over