Variant rs8182488 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001040185.3(ZNF765):c.702G>A(p.Gln234Gln) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.324 in 1,614,056 control chromosomes in the GnomAD database, including 89,951 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 0.26 ( 6545 hom., cov: 33)

Exomes 𝑓: 0.33 ( 83406 hom. )

Consequence

ZNF765
NM_001040185.3 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.389

Variant links:

Genes affected

ZNF765 (HGNC:25092): (zinc finger protein 765) 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 active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ZNF765 links:

ZNF765-ZNF761 (HGNC:):

ZNF765-ZNF761 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=0.389 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.358 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF765	NM_001040185.3 link	c.702G>A	p.Gln234Gln	synonymous_variant	4/4	ENST00000396408.8	NP_001035275.1	Q7L2R6-1
ZNF765	NM_001350495.2 link	c.543G>A	p.Gln181Gln	synonymous_variant	3/3		NP_001337424.1
ZNF765-ZNF761	NM_001350496.2 link	c.-1345+6066G>A		intron_variant			NP_001337425.1
ZNF765	NR_146721.2 link	n.260+6066G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF765	ENST00000396408.8 link	c.702G>A	p.Gln234Gln	synonymous_variant	4/4	1	NM_001040185.3	ENSP00000379689.3		Q7L2R6-1

Frequencies

GnomAD3 genomes

AF:

0.264

AC:

40209

AN:

152078

Hom.:

6535

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0918

Gnomad AMI

AF:

0.387

Gnomad AMR

AF:

0.349

Gnomad ASJ

AF:

0.225

Gnomad EAS

AF:

0.0989

Gnomad SAS

AF:

0.371

Gnomad FIN

AF:

0.367

Gnomad MID

AF:

0.237

Gnomad NFE

AF:

0.341

Gnomad OTH

AF:

0.256

GnomAD3 exomes

AF:

0.320

AC:

80364

AN:

250966

Hom.:

14470

AF XY:

0.323

AC XY:

43841

AN XY:

135820

show subpopulations

Gnomad AFR exome

AF:

0.0816

Gnomad AMR exome

AF:

0.439

Gnomad ASJ exome

AF:

0.218

Gnomad EAS exome

AF:

0.101

Gnomad SAS exome

AF:

0.372

Gnomad FIN exome

AF:

0.372

Gnomad NFE exome

AF:

0.339

Gnomad OTH exome

AF:

0.314

GnomAD4 exome

AF:

0.330

AC:

483074

AN:

1461860

Hom.:

83406

Cov.:

AF XY:

0.332

AC XY:

241107

AN XY:

727230

show subpopulations

Gnomad4 AFR exome

AF:

0.0814

Gnomad4 AMR exome

AF:

0.429

Gnomad4 ASJ exome

AF:

0.219

Gnomad4 EAS exome

AF:

0.0857

Gnomad4 SAS exome

AF:

0.375

Gnomad4 FIN exome

AF:

0.376

Gnomad4 NFE exome

AF:

0.341

Gnomad4 OTH exome

AF:

0.304

GnomAD4 genome

AF:

0.264

AC:

40248

AN:

152196

Hom.:

6545

Cov.:

AF XY:

0.267

AC XY:

19889

AN XY:

74386

show subpopulations

Gnomad4 AFR

AF:

0.0921

Gnomad4 AMR

AF:

0.349

Gnomad4 ASJ

AF:

0.225

Gnomad4 EAS

AF:

0.0987

Gnomad4 SAS

AF:

0.372

Gnomad4 FIN

AF:

0.367

Gnomad4 NFE

AF:

0.341

Gnomad4 OTH

AF:

0.256

Alfa

AF:

0.303

Hom.:

3607

Bravo

AF:

0.250

Asia WGS

AF:

0.251

AC:

870

AN:

3478

EpiCase

AF:

0.323

EpiControl

AF:

0.320

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.59

DANN

Benign

0.86

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