Variant rs11558476 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -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

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:

ZSCAN21 (HGNC:):

ZSCAN21 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
ZSCAN21	NM_145914.3 linkuse as main transcript	c.60G>A	p.Gln20Gln	synonymous_variant	2/4	ENST00000292450.9	NP_666019.1	Q9Y5A6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
ZSCAN21	ENST00000292450.9 linkuse as main transcript	c.60G>A	p.Gln20Gln	synonymous_variant	2/4	1	NM_145914.3	ENSP00000292450.4	Q9Y5A6
ZSCAN21	ENST00000456748.6 linkuse as main transcript	c.60G>A	p.Gln20Gln	synonymous_variant	2/5	5		ENSP00000390960.2	G3V0F4
ZSCAN21	ENST00000438937.1 linkuse as main transcript	c.60G>A	p.Gln20Gln	synonymous_variant	3/4	2		ENSP00000404207.1	C9JHD9
ZSCAN21	ENST00000477297.1 linkuse as main transcript	n.156G>A		non_coding_transcript_exon_variant	1/3	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

GnomAD3 exomes

AF:

0.330

AC:

83049

AN:

251336

Hom.:

14932

AF XY:

0.334

AC XY:

45359

AN XY:

135860

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 SAS exome

AF:

0.409

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

Gnomad4 AFR exome

AF:

0.133

Gnomad4 AMR exome

AF:

0.431

Gnomad4 ASJ exome

AF:

0.371

Gnomad4 EAS exome

AF:

0.484

Gnomad4 SAS exome

AF:

0.404

Gnomad4 FIN exome

AF:

0.285

Gnomad4 NFE exome

AF:

0.279

Gnomad4 OTH exome

AF:

0.317

GnomAD4 genome

AF:

0.269

AC:

40901

AN:

152062

Hom.:

6422

Cov.:

AF XY:

0.277

AC XY:

20560

AN XY:

74314

show subpopulations

Gnomad4 AFR

AF:

0.137

Gnomad4 AMR

AF:

0.403

Gnomad4 ASJ

AF:

0.378

Gnomad4 EAS

AF:

0.455

Gnomad4 SAS

AF:

0.404

Gnomad4 FIN

AF:

0.286

Gnomad4 NFE

AF:

0.285

Gnomad4 OTH

AF:

0.314

Alfa

AF:

0.295

Hom.:

11384

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

DANN

Benign

0.67

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over