Genetic Variant NM_001012455.2: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

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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