Variant 17-50548440-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2

The NM_022827.4(SPATA20):c.283A>G(p.Asn95Asp) variant causes a missense change. The variant allele was found at a frequency of 0.00478 in 1,613,832 control chromosomes in the GnomAD database, including 34 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0040 ( 3 hom., cov: 32)

Exomes 𝑓: 0.0049 ( 31 hom. )

Consequence

SPATA20
NM_022827.4 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 5.79

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 made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.017895311).

BP6

Variant 17-50548440-A-G is Benign according to our data. Variant chr17-50548440-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 2647894.Status of the report is criteria_provided_single_submitter, 1 stars.

BS1

Variant frequency is greater than expected in population mid. gnomad4_exome allele frequency = 0.00486 (7109/1461652) while in subpopulation MID AF= 0.0184 (106/5768). AF 95% confidence interval is 0.0155. There are 31 homozygotes in gnomad4_exome. There are 3536 alleles in male gnomad4_exome subpopulation. Median coverage is 36. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 3 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
SPATA20	NM_022827.4 linkuse as main transcript	c.283A>G	p.Asn95Asp	missense_variant	3/17	ENST00000006658.11	NP_073738.2
SPATA20	NM_001258372.2 linkuse as main transcript	c.235A>G	p.Asn79Asp	missense_variant	2/16		NP_001245301.1
SPATA20	NM_001258373.2 linkuse as main transcript	c.103A>G	p.Asn35Asp	missense_variant	3/17		NP_001245302.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SPATA20	ENST00000006658.11 linkuse as main transcript	c.283A>G	p.Asn95Asp	missense_variant	3/17	1	NM_022827.4	ENSP00000006658		Q8TB22-2

Frequencies

GnomAD3 genomes

AF:

0.00399

AC:

607

AN:

152062

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000990

Gnomad AMI

AF:

0.0504

Gnomad AMR

AF:

0.00426

Gnomad ASJ

AF:

0.0161

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00394

Gnomad FIN

AF:

0.000471

Gnomad MID

AF:

0.0285

Gnomad NFE

AF:

0.00521

Gnomad OTH

AF:

0.00574

GnomAD3 exomes

AF:

0.00416

AC:

1044

AN:

250736

Hom.:

AF XY:

0.00445

AC XY:

604

AN XY:

135710

show subpopulations

Gnomad AFR exome

AF:

0.000802

Gnomad AMR exome

AF:

0.00278

Gnomad ASJ exome

AF:

0.0127

Gnomad EAS exome

AF:

0.000109

Gnomad SAS exome

AF:

0.00399

Gnomad FIN exome

AF:

0.000925

Gnomad NFE exome

AF:

0.00544

Gnomad OTH exome

AF:

0.00785

GnomAD4 exome

AF:

0.00486

AC:

7109

AN:

1461652

Hom.:

Cov.:

AF XY:

0.00486

AC XY:

3536

AN XY:

727132

show subpopulations

Gnomad4 AFR exome

AF:

0.00111

Gnomad4 AMR exome

AF:

0.00327

Gnomad4 ASJ exome

AF:

0.0133

Gnomad4 EAS exome

AF:

0.0000756

Gnomad4 SAS exome

AF:

0.00435

Gnomad4 FIN exome

AF:

0.000937

Gnomad4 NFE exome

AF:

0.00512

Gnomad4 OTH exome

AF:

0.00575

GnomAD4 genome

AF:

0.00398

AC:

606

AN:

152180

Hom.:

Cov.:

AF XY:

0.00370

AC XY:

275

AN XY:

74408

show subpopulations

Gnomad4 AFR

AF:

0.000987

Gnomad4 AMR

AF:

0.00425

Gnomad4 ASJ

AF:

0.0161

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00394

Gnomad4 FIN

AF:

0.000471

Gnomad4 NFE

AF:

0.00521

Gnomad4 OTH

AF:

0.00568

Alfa

AF:

0.00540

Hom.:

Bravo

AF:

0.00444

TwinsUK

AF:

0.00485

AC:

ALSPAC

AF:

0.00285

AC:

ESP6500AA

AF:

0.000681

AC:

ESP6500EA

AF:

0.00558

AC:

ExAC

AF:

0.00418

AC:

507

Asia WGS

AF:

0.00202

AC:

AN:

3478

EpiCase

AF:

0.00709

EpiControl

AF:

0.00759

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Jan 01, 2024

SPATA20: BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Pathogenic

0.75

BayesDel_addAF

Benign

-0.30

BayesDel_noAF

Benign

-0.21

CADD

Uncertain

DANN

Uncertain

1.0

DEOGEN2

Benign

0.31

.;.;T;T

Eigen

Pathogenic

0.71

Eigen_PC

Uncertain

0.63

FATHMM_MKL

Uncertain

0.94

LIST_S2

Pathogenic

0.99

D;D;D;D

M_CAP

Benign

0.036

MetaRNN

Benign

0.018

T;T;T;T

MetaSVM

Benign

-0.39

MutationAssessor

Pathogenic

3.0

.;.;M;.

MutationTaster

Benign

1.0

D;D;D

PrimateAI

Uncertain

0.65

PROVEAN

Pathogenic

-4.6

.;D;D;.

REVEL

Uncertain

0.47

Sift

Pathogenic

0.0

.;D;D;.

Sift4G

Pathogenic

0.0

D;D;D;D

Polyphen

1.0, 1.0

.;D;D;.

Vest4

0.71

MVP

0.69

MPC

0.84

ClinPred

0.053

GERP RS

4.6

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Varity_R

0.84

gMVP

0.70

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

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over