dbSNP rs11635597: ZSCAN2:n.*428C>T (chr15-84622468-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000540894.5(ZSCAN2):n.*428C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.231 in 616,934 control chromosomes in the GnomAD database, including 18,521 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 0.20 ( 3718 hom., cov: 32)

Exomes 𝑓: 0.24 ( 14803 hom. )

Consequence

ZSCAN2
ENST00000540894.5 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.13

Publications

22 publications found

Variant links:

Genes affected

ZSCAN2 (HGNC:20994): (zinc finger and SCAN domain containing 2) The protein encoded by this gene contains several copies of zinc finger motif, which is commonly found in transcriptional regulatory proteins. Studies in mice show that this gene is expressed during embryonic development, and specifically in the testis in adult mice, suggesting that it may play a role in regulating genes in germ cells. Alternative splicing of this gene results in several transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008]

ZSCAN2 links:

ZSCAN2-AS1 (HGNC:56673): (ZSCAN2 antisense RNA 1)

ZSCAN2-AS1 links:

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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=-0.82).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.274 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZSCAN2	NM_181877.4 link	c.*428C>T		3_prime_UTR_variant	Exon 3 of 3	ENST00000546148.6	NP_870992.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZSCAN2	ENST00000546148.6 link	c.*428C>T		3_prime_UTR_variant	Exon 3 of 3	2	NM_181877.4	ENSP00000445451.1

Frequencies

GnomAD3 genomes

AF:

0.196

AC:

29820

AN:

152022

Hom.:

3719

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0481

Gnomad AMI

AF:

0.461

Gnomad AMR

AF:

0.206

Gnomad ASJ

AF:

0.262

Gnomad EAS

AF:

0.126

Gnomad SAS

AF:

0.182

Gnomad FIN

AF:

0.227

Gnomad MID

AF:

0.361

Gnomad NFE

AF:

0.277

Gnomad OTH

AF:

0.219

GnomAD4 exome

AF:

0.243

AC:

112736

AN:

464794

Hom.:

14803

Cov.:

AF XY:

0.243

AC XY:

59744

AN XY:

245570

show subpopulations

African (AFR)

AF:

0.0485

AC:

592

AN:

12208

American (AMR)

AF:

0.192

AC:

3493

AN:

18194

Ashkenazi Jewish (ASJ)

AF:

0.254

AC:

3497

AN:

13772

East Asian (EAS)

AF:

0.103

AC:

3151

AN:

30584

South Asian (SAS)

AF:

0.201

AC:

9089

AN:

45206

European-Finnish (FIN)

AF:

0.223

AC:

9873

AN:

44226

Middle Eastern (MID)

AF:

0.395

AC:

1156

AN:

2924

European-Non Finnish (NFE)

AF:

0.279

AC:

75797

AN:

271446

Other (OTH)

AF:

0.232

AC:

6088

AN:

26234

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

4121

8241

12362

16482

20603

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

340

680

1020

1360

1700

<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:

0.196

AC:

29814

AN:

152140

Hom.:

3718

Cov.:

AF XY:

0.193

AC XY:

14338

AN XY:

74356

show subpopulations

African (AFR)

AF:

0.0480

AC:

1993

AN:

41542

American (AMR)

AF:

0.206

AC:

3152

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.262

AC:

909

AN:

3466

East Asian (EAS)

AF:

0.125

AC:

648

AN:

5170

South Asian (SAS)

AF:

0.183

AC:

881

AN:

4820

European-Finnish (FIN)

AF:

0.227

AC:

2394

AN:

10562

Middle Eastern (MID)

AF:

0.350

AC:

103

AN:

294

European-Non Finnish (NFE)

AF:

0.277

AC:

18858

AN:

67986

Other (OTH)

AF:

0.216

AC:

456

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1161

2323

3484

4646

5807

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

318

636

954

1272

1590

<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:

0.242

Hom.:

4644

Bravo

AF:

0.190

Asia WGS

AF:

0.155

AC:

541

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

5.0

(source)

DANN

Benign

0.63

PhyloP100

-1.1

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