Variant rs10421632 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001023563.4(ZNF805):c.583G>A(p.Val195Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.491 in 1,560,380 control chromosomes in the GnomAD database, including 193,455 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.44 ( 15754 hom., cov: 33)

Exomes 𝑓: 0.50 ( 177701 hom. )

Consequence

ZNF805
NM_001023563.4 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.85

Variant links:

Genes affected

ZNF805 (HGNC:23272): (zinc finger protein 805) 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]

ZNF805 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 (MetaRNN=3.5325684E-5).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.522 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZNF805	NM_001023563.4 linkuse as main transcript	c.583G>A	p.Val195Ile	missense_variant	4/4	ENST00000414468.3	NP_001018857.2
ZNF805	NM_001145078.2 linkuse as main transcript	c.184G>A	p.Val62Ile	missense_variant	3/3		NP_001138550.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZNF805	ENST00000414468.3 linkuse as main transcript	c.583G>A	p.Val195Ile	missense_variant	4/4	5	NM_001023563.4	ENSP00000412999	P1	Q5CZA5-1
ZNF805	ENST00000354309.4 linkuse as main transcript	c.184G>A	p.Val62Ile	missense_variant	3/3	5		ENSP00000365414		Q5CZA5-2

Frequencies

GnomAD3 genomes

AF:

0.437

AC:

66475

AN:

152064

Hom.:

15757

Cov.:

show subpopulations

Gnomad AFR

AF:

0.278

Gnomad AMI

AF:

0.508

Gnomad AMR

AF:

0.443

Gnomad ASJ

AF:

0.539

Gnomad EAS

AF:

0.166

Gnomad SAS

AF:

0.470

Gnomad FIN

AF:

0.552

Gnomad MID

AF:

0.468

Gnomad NFE

AF:

0.526

Gnomad OTH

AF:

0.452

GnomAD3 exomes

AF:

0.467

AC:

78947

AN:

169132

Hom.:

19435

AF XY:

0.474

AC XY:

42670

AN XY:

89988

show subpopulations

Gnomad AFR exome

AF:

0.277

Gnomad AMR exome

AF:

0.424

Gnomad ASJ exome

AF:

0.540

Gnomad EAS exome

AF:

0.157

Gnomad SAS exome

AF:

0.492

Gnomad FIN exome

AF:

0.558

Gnomad NFE exome

AF:

0.520

Gnomad OTH exome

AF:

0.491

GnomAD4 exome

AF:

0.497

AC:

699732

AN:

1408200

Hom.:

177701

Cov.:

AF XY:

0.499

AC XY:

346994

AN XY:

695624

show subpopulations

Gnomad4 AFR exome

AF:

0.274

Gnomad4 AMR exome

AF:

0.422

Gnomad4 ASJ exome

AF:

0.538

Gnomad4 EAS exome

AF:

0.155

Gnomad4 SAS exome

AF:

0.492

Gnomad4 FIN exome

AF:

0.557

Gnomad4 NFE exome

AF:

0.516

Gnomad4 OTH exome

AF:

0.470

GnomAD4 genome

AF:

0.437

AC:

66471

AN:

152180

Hom.:

15754

Cov.:

AF XY:

0.438

AC XY:

32621

AN XY:

74394

show subpopulations

Gnomad4 AFR

AF:

0.278

Gnomad4 AMR

AF:

0.442

Gnomad4 ASJ

AF:

0.539

Gnomad4 EAS

AF:

0.166

Gnomad4 SAS

AF:

0.470

Gnomad4 FIN

AF:

0.552

Gnomad4 NFE

AF:

0.526

Gnomad4 OTH

AF:

0.454

Alfa

AF:

0.495

Hom.:

40235

Bravo

AF:

0.419

TwinsUK

AF:

0.515

AC:

1911

ALSPAC

AF:

0.514

AC:

1980

ESP6500AA

AF:

0.271

AC:

375

ESP6500EA

AF:

0.518

AC:

1647

ExAC

AF:

0.387

AC:

43753

Asia WGS

AF:

0.322

AC:

1117

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.068

BayesDel_addAF

Benign

-0.87

BayesDel_noAF

Benign

-0.87

CADD

Benign

0.0060

DANN

Benign

0.65

DEOGEN2

Benign

0.0018

.;T

Eigen

Benign

-2.2

Eigen_PC

Benign

-2.2

FATHMM_MKL

Benign

0.019

LIST_S2

Benign

0.0033

T;T

MetaRNN

Benign

0.000035

T;T

MetaSVM

Benign

-0.94

MutationAssessor

Benign

0.73

.;N

MutationTaster

Benign

1.0

P;P;P

PrimateAI

Benign

0.26

PROVEAN

Benign

0.13

N;N

REVEL

Benign

0.0090

Sift

Benign

0.79

T;T

Sift4G

Benign

0.45

T;T

Polyphen

0.026

.;B

Vest4

0.024

MPC

0.20

ClinPred

0.012

GERP RS

-8.7

Varity_R

0.028

gMVP

0.012

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