Variant rs4804611 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_145295.4(ZNF627):c.*98A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.259 in 1,042,496 control chromosomes in the GnomAD database, including 35,232 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 0.24 ( 4468 hom., cov: 32)

Exomes 𝑓: 0.26 ( 30764 hom. )

Consequence

ZNF627
NM_145295.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.810

Variant links:

Genes affected

ZNF627 (HGNC:30570): (zinc finger protein 627) Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ZNF627 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.65).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.291 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF627	NM_145295.4 linkuse as main transcript	c.*98A>G		3_prime_UTR_variant	4/4	ENST00000361113.10	NP_660338.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF627	ENST00000361113.10 linkuse as main transcript	c.*98A>G		3_prime_UTR_variant	4/4	1	NM_145295.4	ENSP00000354414	P1
ZNF627	ENST00000588174.1 linkuse as main transcript	c.*1269A>G		3_prime_UTR_variant	4/4	2		ENSP00000465841

Frequencies

GnomAD3 genomes

AF:

0.240

AC:

36423

AN:

152034

Hom.:

4468

Cov.:

show subpopulations

Gnomad AFR

AF:

0.176

Gnomad AMI

AF:

0.270

Gnomad AMR

AF:

0.298

Gnomad ASJ

AF:

0.369

Gnomad EAS

AF:

0.139

Gnomad SAS

AF:

0.237

Gnomad FIN

AF:

0.239

Gnomad MID

AF:

0.297

Gnomad NFE

AF:

0.265

Gnomad OTH

AF:

0.274

GnomAD4 exome

AF:

0.262

AC:

233095

AN:

890346

Hom.:

30764

Cov.:

AF XY:

0.262

AC XY:

117401

AN XY:

448010

show subpopulations

Gnomad4 AFR exome

AF:

0.177

Gnomad4 AMR exome

AF:

0.303

Gnomad4 ASJ exome

AF:

0.363

Gnomad4 EAS exome

AF:

0.128

Gnomad4 SAS exome

AF:

0.240

Gnomad4 FIN exome

AF:

0.231

Gnomad4 NFE exome

AF:

0.270

Gnomad4 OTH exome

AF:

0.262

GnomAD4 genome

AF:

0.239

AC:

36435

AN:

152150

Hom.:

4468

Cov.:

AF XY:

0.242

AC XY:

17977

AN XY:

74394

show subpopulations

Gnomad4 AFR

AF:

0.176

Gnomad4 AMR

AF:

0.298

Gnomad4 ASJ

AF:

0.369

Gnomad4 EAS

AF:

0.139

Gnomad4 SAS

AF:

0.238

Gnomad4 FIN

AF:

0.239

Gnomad4 NFE

AF:

0.265

Gnomad4 OTH

AF:

0.273

Alfa

AF:

0.245

Hom.:

3004

Bravo

AF:

0.241

Asia WGS

AF:

0.197

AC:

683

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.65

CADD

Benign

3.9

DANN

Benign

0.68

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