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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_198546.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
SPATA21	NM_198546.1	MANE Select	c.812-48G>C	intron	N/A	NP_940948.1	Q7Z572-1
SPATA21	NM_001353349.1		c.743-48G>C	intron	N/A	NP_001340278.1	Q7Z572-2
SPATA21	NR_148413.2		n.1927-48G>C	intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
SPATA21	ENST00000335496.5	TSL:1 MANE Select	c.812-48G>C	intron	N/A	ENSP00000335612.1	Q7Z572-1
SPATA21	ENST00000540400.1	TSL:1	c.743-48G>C	intron	N/A	ENSP00000440046.1	Q7Z572-2
SPATA21	ENST00000466212.5	TSL:2	n.2104-48G>C	intron	N/A

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 v4.9

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over