Variant 8-7860744-A-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_001395484.1(SPAG11A):c.313A>T(p.Ser105Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 10/12 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.92 ( 50325 hom., cov: 19)

Exomes 𝑓: 0.99 ( 626521 hom. )

Failed GnomAD Quality Control

Consequence

SPAG11A
NM_001395484.1 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.48

Variant links:

Genes affected

SPAG11A (HGNC:33342): (sperm associated antigen 11A) Involved in antimicrobial humoral immune response mediated by antimicrobial peptide and cytolysis by host of symbiont cells. Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Apr 2022]

SPAG11A 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=5.8364196E-7).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.991 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
SPAG11A	NM_001395484.1 linkuse as main transcript	c.313A>T	p.Ser105Cys	missense_variant	3/3	ENST00000642566.2
SPAG11A	XM_017013744.2 linkuse as main transcript	c.154A>T	p.Ser52Cys	missense_variant	2/2
SPAG11A	NM_001363726.3 linkuse as main transcript	c.*77A>T		3_prime_UTR_variant	4/4
SPAG11A	NM_001081552.3 linkuse as main transcript	c.292+21A>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SPAG11A	ENST00000642566.2 linkuse as main transcript	c.313A>T	p.Ser105Cys	missense_variant	3/3		NM_001395484.1	P3

Frequencies

GnomAD3 genomes

AF:

0.921

AC:

108297

AN:

117622

Hom.:

50286

Cov.:

show subpopulations

Gnomad AFR

AF:

0.752

Gnomad AMI

AF:

1.00

Gnomad AMR

AF:

0.969

Gnomad ASJ

AF:

1.00

Gnomad EAS

AF:

1.00

Gnomad SAS

AF:

0.998

Gnomad FIN

AF:

1.00

Gnomad MID

AF:

0.973

Gnomad NFE

AF:

0.999

Gnomad OTH

AF:

0.940

GnomAD3 exomes

AF:

0.980

AC:

193179

AN:

197214

Hom.:

95001

AF XY:

0.984

AC XY:

104060

AN XY:

105708

show subpopulations

Gnomad AFR exome

AF:

0.760

Gnomad AMR exome

AF:

0.986

Gnomad ASJ exome

AF:

1.00

Gnomad EAS exome

AF:

1.00

Gnomad SAS exome

AF:

1.00

Gnomad FIN exome

AF:

1.00

Gnomad NFE exome

AF:

0.999

Gnomad OTH exome

AF:

0.987

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.993

AC:

1259962

AN:

1269122

Hom.:

626521

Cov.:

AF XY:

0.994

AC XY:

624569

AN XY:

628520

show subpopulations

Gnomad4 AFR exome

AF:

0.765

Gnomad4 AMR exome

AF:

0.984

Gnomad4 ASJ exome

AF:

1.00

Gnomad4 EAS exome

AF:

1.00

Gnomad4 SAS exome

AF:

1.00

Gnomad4 FIN exome

AF:

1.00

Gnomad4 NFE exome

AF:

0.999

Gnomad4 OTH exome

AF:

0.984

GnomAD4 genome

AF:

0.921

AC:

108391

AN:

117732

Hom.:

50325

Cov.:

AF XY:

0.922

AC XY:

51898

AN XY:

56258

show subpopulations

Gnomad4 AFR

AF:

0.752

Gnomad4 AMR

AF:

0.969

Gnomad4 ASJ

AF:

1.00

Gnomad4 EAS

AF:

1.00

Gnomad4 SAS

AF:

0.998

Gnomad4 FIN

AF:

1.00

Gnomad4 NFE

AF:

0.999

Gnomad4 OTH

AF:

0.941

Alfa

AF:

0.952

Hom.:

6410

ExAC

AF:

0.975

AC:

105551

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.74

BayesDel_noAF

Benign

-0.69

CADD

Benign

DANN

Benign

0.074

DEOGEN2

Benign

0.0022

.;T

Eigen

Benign

-0.84

Eigen_PC

Benign

-0.75

FATHMM_MKL

Benign

0.0055

LIST_S2

Benign

0.25

T;T

MetaRNN

Benign

5.8e-7

T;T

MetaSVM

Benign

-0.96

MutationTaster

Benign

1.0

P;P;P;P;P

PROVEAN

Benign

8.1

.;N

REVEL

Benign

0.086

Sift

Benign

1.0

.;T

Sift4G

Benign

1.0

.;T

Vest4

0.081

ClinPred

0.0062

GERP RS

2.3

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