dbSNP rs17419150: SPATA21:c.812-48G>C (chr1-16404087-C-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_198546.1(SPATA21):c.812-48G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.39 in 1,502,446 control chromosomes in the GnomAD database, including 120,018 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 0.34 ( 10054 hom., cov: 31)

Exomes 𝑓: 0.40 ( 109964 hom. )

Consequence

SPATA21
NM_198546.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0460

Publications

13 publications found

Variant links:

Genes affected

SPATA21 (HGNC:28026): (spermatogenesis associated 21) Predicted to enable calcium ion binding activity. [provided by Alliance of Genome Resources, Apr 2022]

SPATA21 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.657 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SPATA21	NM_198546.1 link	c.812-48G>C		intron_variant	Intron 8 of 12	ENST00000335496.5	NP_940948.1	Q7Z572-1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
SPATA21	ENST00000335496.5 link	c.812-48G>C	intron_variant	Intron 8 of 12	1	NM_198546.1	ENSP00000335612.1	Q7Z572-1
SPATA21	ENST00000540400.1 link	c.743-48G>C	intron_variant	Intron 6 of 10	1		ENSP00000440046.1	Q7Z572-2
SPATA21	ENST00000466212.5 link	n.2104-48G>C	intron_variant	Intron 10 of 16	2
SPATA21	ENST00000491418.5 link	c.-113G>C	upstream_gene_variant		5		ENSP00000420753.1	H7C5T0

Frequencies

GnomAD3 genomes

AF:

0.339

AC:

51538

AN:

151880

Hom.:

10062

Cov.:

show subpopulations

Gnomad AFR

AF:

0.146

Gnomad AMI

AF:

0.398

Gnomad AMR

AF:

0.332

Gnomad ASJ

AF:

0.365

Gnomad EAS

AF:

0.676

Gnomad SAS

AF:

0.399

Gnomad FIN

AF:

0.523

Gnomad MID

AF:

0.370

Gnomad NFE

AF:

0.397

Gnomad OTH

AF:

0.353

GnomAD2 exomes

AF:

0.407

AC:

63643

AN:

156306

AF XY:

0.411

show subpopulations

Gnomad AFR exome

AF:

0.139

Gnomad AMR exome

AF:

0.357

Gnomad ASJ exome

AF:

0.361

Gnomad EAS exome

AF:

0.692

Gnomad FIN exome

AF:

0.524

Gnomad NFE exome

AF:

0.395

Gnomad OTH exome

AF:

0.391

GnomAD4 exome

AF:

0.396

AC:

534407

AN:

1350448

Hom.:

109964

Cov.:

AF XY:

0.397

AC XY:

265314

AN XY:

669122

show subpopulations

African (AFR)

AF:

0.135

AC:

4108

AN:

30504

American (AMR)

AF:

0.353

AC:

12557

AN:

35608

Ashkenazi Jewish (ASJ)

AF:

0.358

AC:

8917

AN:

24896

East Asian (EAS)

AF:

0.699

AC:

24799

AN:

35486

South Asian (SAS)

AF:

0.397

AC:

31053

AN:

78204

European-Finnish (FIN)

AF:

0.520

AC:

25601

AN:

49222

Middle Eastern (MID)

AF:

0.361

AC:

1713

AN:

4744

European-Non Finnish (NFE)

AF:

0.390

AC:

403439

AN:

1035552

Other (OTH)

AF:

0.395

AC:

22220

AN:

56232

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

16125

32250

48374

64499

80624

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

12474

24948

37422

49896

62370

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.339

AC:

51531

AN:

151998

Hom.:

10054

Cov.:

AF XY:

0.347

AC XY:

25795

AN XY:

74286

show subpopulations

African (AFR)

AF:

0.146

AC:

6058

AN:

41470

American (AMR)

AF:

0.332

AC:

5070

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.365

AC:

1267

AN:

3468

East Asian (EAS)

AF:

0.676

AC:

3493

AN:

5170

South Asian (SAS)

AF:

0.399

AC:

1920

AN:

4810

European-Finnish (FIN)

AF:

0.523

AC:

5522

AN:

10566

Middle Eastern (MID)

AF:

0.371

AC:

109

AN:

294

European-Non Finnish (NFE)

AF:

0.397

AC:

26994

AN:

67930

Other (OTH)

AF:

0.350

AC:

737

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

1682

3364

5046

6728

8410

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

516

1032

1548

2064

2580

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.368

Hom.:

2033

Bravo

AF:

0.320

Asia WGS

AF:

0.467

AC:

1622

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

3.6

(source)

DANN

Benign

0.53

PhyloP100

0.046

PromoterAI

-0.056

Neutral

(source)

Mutation Taster

=100/0

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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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