Variant rs17774663 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The ENST00000330236.7(ZKSCAN8):c.840G>A(p.Gln280=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.224 in 1,613,966 control chromosomes in the GnomAD database, including 41,666 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 0.23 ( 4152 hom., cov: 32)

Exomes 𝑓: 0.22 ( 37514 hom. )

Consequence

ZKSCAN8
ENST00000330236.7 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.46

Variant links:

Genes affected

ZKSCAN8 (HGNC:12983): (zinc finger with KRAB and SCAN domains 8) Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific 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]

ZKSCAN8 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=-0.9).

BP7

Synonymous conserved (PhyloP=-2.46 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.279 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZKSCAN8	NM_006298.4 linkuse as main transcript	c.840G>A	p.Gln280=	synonymous_variant	6/6	ENST00000330236.7	NP_006289.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZKSCAN8	ENST00000330236.7 linkuse as main transcript	c.840G>A	p.Gln280=	synonymous_variant	6/6	1	NM_006298.4	ENSP00000332750	P1	Q15776-1
ZKSCAN8	ENST00000457389.6 linkuse as main transcript	c.840G>A	p.Gln280=	synonymous_variant	7/7	1		ENSP00000402948	P1	Q15776-1
ZKSCAN8	ENST00000606198.5 linkuse as main transcript	c.*377G>A		3_prime_UTR_variant, NMD_transcript_variant	6/6	1		ENSP00000475589		Q15776-2
ZKSCAN8	ENST00000536028.2 linkuse as main transcript			downstream_gene_variant		2		ENSP00000439117		Q15776-2

Frequencies

GnomAD3 genomes

AF:

0.229

AC:

34865

AN:

151986

Hom.:

4145

Cov.:

show subpopulations

Gnomad AFR

AF:

0.284

Gnomad AMI

AF:

0.289

Gnomad AMR

AF:

0.241

Gnomad ASJ

AF:

0.169

Gnomad EAS

AF:

0.174

Gnomad SAS

AF:

0.141

Gnomad FIN

AF:

0.183

Gnomad MID

AF:

0.130

Gnomad NFE

AF:

0.214

Gnomad OTH

AF:

0.222

GnomAD3 exomes

AF:

0.204

AC:

51189

AN:

251422

Hom.:

5525

AF XY:

0.198

AC XY:

26932

AN XY:

135880

show subpopulations

Gnomad AFR exome

AF:

0.281

Gnomad AMR exome

AF:

0.239

Gnomad ASJ exome

AF:

0.178

Gnomad EAS exome

AF:

0.164

Gnomad SAS exome

AF:

0.139

Gnomad FIN exome

AF:

0.187

Gnomad NFE exome

AF:

0.212

Gnomad OTH exome

AF:

0.189

GnomAD4 exome

AF:

0.223

AC:

325845

AN:

1461862

Hom.:

37514

Cov.:

AF XY:

0.219

AC XY:

159492

AN XY:

727234

show subpopulations

Gnomad4 AFR exome

AF:

0.284

Gnomad4 AMR exome

AF:

0.237

Gnomad4 ASJ exome

AF:

0.173

Gnomad4 EAS exome

AF:

0.218

Gnomad4 SAS exome

AF:

0.139

Gnomad4 FIN exome

AF:

0.185

Gnomad4 NFE exome

AF:

0.232

Gnomad4 OTH exome

AF:

0.205

GnomAD4 genome

AF:

0.229

AC:

34901

AN:

152104

Hom.:

4152

Cov.:

AF XY:

0.224

AC XY:

16624

AN XY:

74338

show subpopulations

Gnomad4 AFR

AF:

0.284

Gnomad4 AMR

AF:

0.242

Gnomad4 ASJ

AF:

0.169

Gnomad4 EAS

AF:

0.175

Gnomad4 SAS

AF:

0.143

Gnomad4 FIN

AF:

0.183

Gnomad4 NFE

AF:

0.214

Gnomad4 OTH

AF:

0.219

Alfa

AF:

0.223

Hom.:

2596

Bravo

AF:

0.240

Asia WGS

AF:

0.154

AC:

537

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

0.056

DANN

Benign

0.30

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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