dbSNP rs11558476: ZSCAN21:p.Gln20Gln (chr7-100057066-G-A) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_145914.3(ZSCAN21):c.60G>A(p.Gln20Gln) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.295 in 1,613,822 control chromosomes in the GnomAD database, including 74,350 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 0.27 ( 6422 hom., cov: 32)

Exomes 𝑓: 0.30 ( 67928 hom. )

Consequence

ZSCAN21
NM_145914.3 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.403

Publications

24 publications found

Variant links:

Genes affected

ZSCAN21 (HGNC:13104): (zinc finger and SCAN domain containing 21) Enables DNA-binding transcription activator activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Involved in positive regulation of transcription by RNA polymerase II. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ZSCAN21 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.71).

BP7

Synonymous conserved (PhyloP=-0.403 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.44 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZSCAN21	NM_145914.3 link	c.60G>A	p.Gln20Gln	synonymous_variant	Exon 2 of 4	ENST00000292450.9	NP_666019.1	Q9Y5A6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
ZSCAN21	ENST00000292450.9 link	c.60G>A	p.Gln20Gln	synonymous_variant	Exon 2 of 4	1	NM_145914.3	ENSP00000292450.4	Q9Y5A6
ZSCAN21	ENST00000456748.6 link	c.60G>A	p.Gln20Gln	synonymous_variant	Exon 2 of 5	5		ENSP00000390960.2	G3V0F4
ZSCAN21	ENST00000438937.1 link	c.60G>A	p.Gln20Gln	synonymous_variant	Exon 3 of 4	2		ENSP00000404207.1	C9JHD9
ZSCAN21	ENST00000477297.1 link	n.156G>A		non_coding_transcript_exon_variant	Exon 1 of 3	3

Frequencies

GnomAD3 genomes

AF:

0.269

AC:

40887

AN:

151946

Hom.:

6425

Cov.:

show subpopulations

Gnomad AFR

AF:

0.137

Gnomad AMI

AF:

0.311

Gnomad AMR

AF:

0.403

Gnomad ASJ

AF:

0.378

Gnomad EAS

AF:

0.456

Gnomad SAS

AF:

0.403

Gnomad FIN

AF:

0.286

Gnomad MID

AF:

0.465

Gnomad NFE

AF:

0.285

Gnomad OTH

AF:

0.313

GnomAD2 exomes

AF:

0.330

AC:

83049

AN:

251336

AF XY:

0.334

show subpopulations

Gnomad AFR exome

AF:

0.134

Gnomad AMR exome

AF:

0.430

Gnomad ASJ exome

AF:

0.376

Gnomad EAS exome

AF:

0.486

Gnomad FIN exome

AF:

0.286

Gnomad NFE exome

AF:

0.286

Gnomad OTH exome

AF:

0.346

GnomAD4 exome

AF:

0.297

AC:

434816

AN:

1461760

Hom.:

67928

Cov.:

AF XY:

0.302

AC XY:

219855

AN XY:

727178

show subpopulations

African (AFR)

AF:

0.133

AC:

4455

AN:

33476

American (AMR)

AF:

0.431

AC:

19274

AN:

44724

Ashkenazi Jewish (ASJ)

AF:

0.371

AC:

9688

AN:

26136

East Asian (EAS)

AF:

0.484

AC:

19220

AN:

39700

South Asian (SAS)

AF:

0.404

AC:

34840

AN:

86254

European-Finnish (FIN)

AF:

0.285

AC:

15212

AN:

53386

Middle Eastern (MID)

AF:

0.500

AC:

2871

AN:

5742

European-Non Finnish (NFE)

AF:

0.279

AC:

310104

AN:

1111956

Other (OTH)

AF:

0.317

AC:

19152

AN:

60386

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.478

Heterozygous variant carriers

17582

35164

52746

70328

87910

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

10462

20924

31386

41848

52310

<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:

0.269

AC:

40901

AN:

152062

Hom.:

6422

Cov.:

AF XY:

0.277

AC XY:

20560

AN XY:

74314

show subpopulations

African (AFR)

AF:

0.137

AC:

5695

AN:

41534

American (AMR)

AF:

0.403

AC:

6155

AN:

15256

Ashkenazi Jewish (ASJ)

AF:

0.378

AC:

1309

AN:

3466

East Asian (EAS)

AF:

0.455

AC:

2346

AN:

5156

South Asian (SAS)

AF:

0.404

AC:

1944

AN:

4816

European-Finnish (FIN)

AF:

0.286

AC:

3020

AN:

10574

Middle Eastern (MID)

AF:

0.463

AC:

136

AN:

294

European-Non Finnish (NFE)

AF:

0.285

AC:

19351

AN:

67948

Other (OTH)

AF:

0.314

AC:

663

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

1414

2828

4243

5657

7071

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

420

840

1260

1680

2100

<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:

0.293

Hom.:

14530

Bravo

AF:

0.274

Asia WGS

AF:

0.389

AC:

1351

AN:

3478

EpiCase

AF:

0.304

EpiControl

AF:

0.309

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.71

CADD

Benign

2.7

(source)

DANN

Benign

0.67

PhyloP100

-0.40

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