Genetic Variant ZSCAN23:c.408+33A>G (chr6-28435826-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_001012455.2(ZSCAN23):c.408+33A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.389 in 1,522,896 control chromosomes in the GnomAD database, including 117,749 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 0.39 ( 12237 hom., cov: 32)

Exomes 𝑓: 0.39 ( 105512 hom. )

Consequence

ZSCAN23
NM_001012455.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.88

Publications

25 publications found

Variant links:

Genes affected

ZSCAN23 (HGNC:21193): (zinc finger and SCAN domain containing 23) Enables sequence-specific double-stranded DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ZSCAN23 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=-1.02).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.494 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZSCAN23	NM_001012455.2 link	c.408+33A>G		intron_variant	Intron 2 of 3	ENST00000289788.5	NP_001012458.1	Q3MJ62

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
ZSCAN23	ENST00000289788.5 link	c.408+33A>G	intron_variant	Intron 2 of 3	1	NM_001012455.2	ENSP00000289788.4	Q3MJ62
ZSCAN23	ENST00000481983.5 link	n.408+33A>G	intron_variant	Intron 2 of 3	5		ENSP00000435430.1	G3V1D5
ZSCAN23	ENST00000486481.1 link	n.105-219A>G	intron_variant	Intron 1 of 2	2

Frequencies

GnomAD3 genomes

AF:

0.393

AC:

59698

AN:

151950

Hom.:

12217

Cov.:

show subpopulations

Gnomad AFR

AF:

0.500

Gnomad AMI

AF:

0.348

Gnomad AMR

AF:

0.371

Gnomad ASJ

AF:

0.407

Gnomad EAS

AF:

0.274

Gnomad SAS

AF:

0.379

Gnomad FIN

AF:

0.266

Gnomad MID

AF:

0.335

Gnomad NFE

AF:

0.362

Gnomad OTH

AF:

0.406

GnomAD2 exomes

AF:

0.351

AC:

57862

AN:

164706

AF XY:

0.349

show subpopulations

Gnomad AFR exome

AF:

0.503

Gnomad AMR exome

AF:

0.337

Gnomad ASJ exome

AF:

0.442

Gnomad EAS exome

AF:

0.252

Gnomad FIN exome

AF:

0.267

Gnomad NFE exome

AF:

0.355

Gnomad OTH exome

AF:

0.362

GnomAD4 exome

AF:

0.388

AC:

532470

AN:

1370828

Hom.:

105512

Cov.:

AF XY:

0.387

AC XY:

260370

AN XY:

673592

show subpopulations

African (AFR)

AF:

0.508

AC:

15392

AN:

30284

American (AMR)

AF:

0.347

AC:

9724

AN:

28016

Ashkenazi Jewish (ASJ)

AF:

0.426

AC:

8692

AN:

20410

East Asian (EAS)

AF:

0.292

AC:

11292

AN:

38696

South Asian (SAS)

AF:

0.381

AC:

26839

AN:

70428

European-Finnish (FIN)

AF:

0.268

AC:

13343

AN:

49782

Middle Eastern (MID)

AF:

0.326

AC:

1747

AN:

5354

European-Non Finnish (NFE)

AF:

0.395

AC:

423231

AN:

1071290

Other (OTH)

AF:

0.393

AC:

22210

AN:

56568

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.496

Heterozygous variant carriers

17542

35085

52627

70170

87712

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

13888

27776

41664

55552

69440

<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:

0.393

AC:

59768

AN:

152068

Hom.:

12237

Cov.:

AF XY:

0.385

AC XY:

28607

AN XY:

74334

show subpopulations

African (AFR)

AF:

0.500

AC:

20730

AN:

41460

American (AMR)

AF:

0.371

AC:

5673

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.407

AC:

1409

AN:

3466

East Asian (EAS)

AF:

0.274

AC:

1419

AN:

5170

South Asian (SAS)

AF:

0.381

AC:

1834

AN:

4810

European-Finnish (FIN)

AF:

0.266

AC:

2822

AN:

10592

Middle Eastern (MID)

AF:

0.333

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.362

AC:

24616

AN:

67982

Other (OTH)

AF:

0.403

AC:

850

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1811

3621

5432

7242

9053

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

576

1152

1728

2304

2880

<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:

0.383

Hom.:

19938

Bravo

AF:

0.405

Asia WGS

AF:

0.349

AC:

1216

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.071

(source)

DANN

Benign

0.50

PhyloP100

-3.9

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

Details are displayed if max score is > 0.2

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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