Genetic Variant SPAG11A:p.Ser105Cys (chr8-7860744-A-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -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. 11/14 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

Publications

6 publications found

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:

LOC124901865 (HGNC:):

LOC124901865 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
SPAG11A	NM_001395484.1 link	c.313A>T	p.Ser105Cys	missense_variant	Exon 3 of 3	ENST00000642566.2	NP_001382413.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SPAG11A	ENST00000642566.2 link	c.313A>T	p.Ser105Cys	missense_variant	Exon 3 of 3		NM_001395484.1	ENSP00000496500.1		A0A2R8Y853

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

GnomAD2 exomes

AF:

0.980

AC:

193179

AN:

197214

AF XY:

0.984

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 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

African (AFR)

AF:

0.765

AC:

22562

AN:

29492

American (AMR)

AF:

0.984

AC:

37255

AN:

37862

Ashkenazi Jewish (ASJ)

AF:

1.00

AC:

21553

AN:

21556

East Asian (EAS)

AF:

1.00

AC:

28626

AN:

28626

South Asian (SAS)

AF:

1.00

AC:

65529

AN:

65556

European-Finnish (FIN)

AF:

1.00

AC:

46420

AN:

46424

Middle Eastern (MID)

AF:

0.992

AC:

5093

AN:

5136

European-Non Finnish (NFE)

AF:

0.999

AC:

981463

AN:

982150

Other (OTH)

AF:

0.984

AC:

51461

AN:

52320

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.424

Heterozygous variant carriers

208

416

624

832

1040

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.921

AC:

108391

AN:

117732

Hom.:

50325

Cov.:

AF XY:

0.922

AC XY:

51898

AN XY:

56258

show subpopulations

African (AFR)

AF:

0.752

AC:

26729

AN:

35526

American (AMR)

AF:

0.969

AC:

11461

AN:

11822

Ashkenazi Jewish (ASJ)

AF:

1.00

AC:

2678

AN:

2678

East Asian (EAS)

AF:

1.00

AC:

2690

AN:

2690

South Asian (SAS)

AF:

0.998

AC:

2779

AN:

2784

European-Finnish (FIN)

AF:

1.00

AC:

7172

AN:

7172

Middle Eastern (MID)

AF:

0.975

AC:

232

AN:

238

European-Non Finnish (NFE)

AF:

0.999

AC:

52476

AN:

52554

Other (OTH)

AF:

0.941

AC:

1502

AN:

1596

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.519

Heterozygous variant carriers

216

432

648

864

1080

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

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

(source)

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

PhyloP100

1.5

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

Mutation Taster

=97/3

polymorphism (auto)

(source)

Splicing

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

Publications

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8-7860744-A-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