Variant 10-45626438-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_174890.4(ZFAND4):c.1385G>A(p.Arg462Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00842 in 1,613,694 control chromosomes in the GnomAD database, including 80 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0065 ( 8 hom., cov: 32)

Exomes 𝑓: 0.0086 ( 72 hom. )

Consequence

ZFAND4
NM_174890.4 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.251

Variant links:

Genes affected

ZFAND4 (HGNC:23504): (zinc finger AN1-type containing 4) Predicted to enable zinc ion binding activity. [provided by Alliance of Genome Resources, Apr 2022]

ZFAND4 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.003657043).

BP6

Variant 10-45626438-C-T is Benign according to our data. Variant chr10-45626438-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2640424.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd4 at 8 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZFAND4	NM_174890.4 linkuse as main transcript	c.1385G>A	p.Arg462Gln	missense_variant	7/10	ENST00000344646.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris
ZFAND4	ENST00000344646.10 linkuse as main transcript	c.1385G>A	p.Arg462Gln	missense_variant	7/10	1	NM_174890.4	P1
ZFAND4	ENST00000374366.7 linkuse as main transcript	c.1163G>A	p.Arg388Gln	missense_variant	8/11	1
ZFAND4	ENST00000374371.6 linkuse as main transcript	c.570-8178G>A		intron_variant		5
ZFAND4	ENST00000374370.1 linkuse as main transcript	n.1105G>A		non_coding_transcript_exon_variant	4/7	2

Frequencies

GnomAD3 genomes

AF:

0.00655

AC:

996

AN:

152132

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00167

Gnomad AMI

AF:

0.00768

Gnomad AMR

AF:

0.00190

Gnomad ASJ

AF:

0.00144

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00746

Gnomad FIN

AF:

0.0223

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.00894

Gnomad OTH

AF:

0.00239

GnomAD3 exomes

AF:

0.00694

AC:

1726

AN:

248800

Hom.:

AF XY:

0.00714

AC XY:

963

AN XY:

134808

show subpopulations

Gnomad AFR exome

AF:

0.00162

Gnomad AMR exome

AF:

0.00148

Gnomad ASJ exome

AF:

0.000401

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00717

Gnomad FIN exome

AF:

0.0206

Gnomad NFE exome

AF:

0.00855

Gnomad OTH exome

AF:

0.00477

GnomAD4 exome

AF:

0.00861

AC:

12589

AN:

1461444

Hom.:

Cov.:

AF XY:

0.00847

AC XY:

6159

AN XY:

727036

show subpopulations

Gnomad4 AFR exome

AF:

0.00164

Gnomad4 AMR exome

AF:

0.00181

Gnomad4 ASJ exome

AF:

0.000574

Gnomad4 EAS exome

AF:

0.0000504

Gnomad4 SAS exome

AF:

0.00730

Gnomad4 FIN exome

AF:

0.0200

Gnomad4 NFE exome

AF:

0.00932

Gnomad4 OTH exome

AF:

0.00623

GnomAD4 genome

AF:

0.00654

AC:

995

AN:

152250

Hom.:

Cov.:

AF XY:

0.00700

AC XY:

521

AN XY:

74430

show subpopulations

Gnomad4 AFR

AF:

0.00166

Gnomad4 AMR

AF:

0.00183

Gnomad4 ASJ

AF:

0.00144

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00746

Gnomad4 FIN

AF:

0.0223

Gnomad4 NFE

AF:

0.00894

Gnomad4 OTH

AF:

0.00237

Alfa

AF:

0.00747

Hom.:

Bravo

AF:

0.00434

TwinsUK

AF:

0.00809

AC:

ALSPAC

AF:

0.0104

AC:

ESP6500AA

AF:

0.00113

AC:

ESP6500EA

AF:

0.00674

AC:

ExAC

AF:

0.00704

AC:

855

Asia WGS

AF:

0.00375

AC:

AN:

3478

EpiCase

AF:

0.00616

EpiControl

AF:

0.00652

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Jan 01, 2023

ZFAND4: BP4, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.089

BayesDel_addAF

Benign

-0.42

BayesDel_noAF

Benign

-0.37

CADD

Benign

DANN

Uncertain

1.0

Eigen

Benign

-0.014

Eigen_PC

Benign

-0.010

FATHMM_MKL

Benign

0.58

LIST_S2

Benign

0.71

T;T

MetaRNN

Benign

0.0037

T;T

MetaSVM

Benign

-1.0

MutationTaster

Benign

0.81

D;D;D;D

PrimateAI

Benign

0.31

PROVEAN

Benign

-0.74

N;N

REVEL

Benign

0.14

Sift

Uncertain

0.026

D;D

Sift4G

Benign

0.54

T;T

Polyphen

0.80

.;P

Vest4

0.23

MVP

0.20

MPC

0.15

ClinPred

0.015

GERP RS

4.6

Varity_R

0.052

gMVP

0.21

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over