Genetic Variant ZSCAN2:c.407-3838T>C (chr15-84616764-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_181877.4(ZSCAN2):c.407-3838T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.845 in 841,500 control chromosomes in the GnomAD database, including 301,073 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 0.86 ( 56716 hom., cov: 32)

Exomes 𝑓: 0.84 ( 244357 hom. )

Consequence

ZSCAN2
NM_181877.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0760

Publications

8 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:

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=-0.9).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.912 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZSCAN2	NM_181877.4 link	c.407-3838T>C		intron_variant	Intron 2 of 2	ENST00000546148.6	NP_870992.2	Q7Z7L9-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZSCAN2	ENST00000546148.6 link	c.407-3838T>C		intron_variant	Intron 2 of 2	2	NM_181877.4	ENSP00000445451.1		Q7Z7L9-1

Frequencies

GnomAD3 genomes

AF:

0.862

AC:

131125

AN:

152090

Hom.:

56673

Cov.:

show subpopulations

Gnomad AFR

AF:

0.920

Gnomad AMI

AF:

0.915

Gnomad AMR

AF:

0.773

Gnomad ASJ

AF:

0.877

Gnomad EAS

AF:

0.933

Gnomad SAS

AF:

0.823

Gnomad FIN

AF:

0.833

Gnomad MID

AF:

0.867

Gnomad NFE

AF:

0.848

Gnomad OTH

AF:

0.841

GnomAD4 exome

AF:

0.841

AC:

579692

AN:

689292

Hom.:

244357

AF XY:

0.841

AC XY:

270490

AN XY:

321706

show subpopulations

African (AFR)

AF:

0.933

AC:

11946

AN:

12808

American (AMR)

AF:

0.718

AC:

655

AN:

912

Ashkenazi Jewish (ASJ)

AF:

0.871

AC:

3789

AN:

4348

East Asian (EAS)

AF:

0.930

AC:

2831

AN:

3044

South Asian (SAS)

AF:

0.829

AC:

11408

AN:

13764

European-Finnish (FIN)

AF:

0.802

AC:

401

AN:

500

Middle Eastern (MID)

AF:

0.844

AC:

1128

AN:

1336

European-Non Finnish (NFE)

AF:

0.839

AC:

528376

AN:

629970

Other (OTH)

AF:

0.847

AC:

19158

AN:

22610

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

4227

8454

12682

16909

21136

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.862

AC:

131223

AN:

152208

Hom.:

56716

Cov.:

AF XY:

0.859

AC XY:

63939

AN XY:

74412

show subpopulations

African (AFR)

AF:

0.920

AC:

38226

AN:

41546

American (AMR)

AF:

0.772

AC:

11796

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.877

AC:

3040

AN:

3468

East Asian (EAS)

AF:

0.933

AC:

4833

AN:

5182

South Asian (SAS)

AF:

0.824

AC:

3977

AN:

4826

European-Finnish (FIN)

AF:

0.833

AC:

8825

AN:

10590

Middle Eastern (MID)

AF:

0.871

AC:

256

AN:

294

European-Non Finnish (NFE)

AF:

0.848

AC:

57669

AN:

68006

Other (OTH)

AF:

0.837

AC:

1770

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

937

1874

2812

3749

4686

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.845

Hom.:

88861

Bravo

AF:

0.860

Asia WGS

AF:

0.876

AC:

3046

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

8.5

(source)

DANN

Benign

0.80

PhyloP100

-0.076

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

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

15-84616764-T-C

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