Variant rs35303725 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The ENST00000382409.4(DEAF1):c.1401G>A(p.Ala467=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0189 in 1,614,138 control chromosomes in the GnomAD database, including 536 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.014 ( 34 hom., cov: 33)

Exomes 𝑓: 0.019 ( 502 hom. )

Consequence

DEAF1
ENST00000382409.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: -3.78

Variant links:

Genes affected

DEAF1 (HGNC:14677): (DEAF1 transcription factor) This gene encodes a zinc finger domain-containing protein that functions as a regulator of transcription. The encoded proteins binds to its own promoter as well as to that of several target genes. Activity of this protein is important in the regulation of embryonic development. Mutations in this gene have been found in individuals with autosomal dominant cognitive disability. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jun 2014]

DEAF1 links:

(HGNC:):

links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.69).

BP6

Variant 11-674638-C-T is Benign according to our data. Variant chr11-674638-C-T is described in ClinVar as [Benign]. Clinvar id is 585771.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-3.78 with no splicing effect.

BA1

GnomAdExome4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0642 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DEAF1	NM_021008.4 linkuse as main transcript	c.1401G>A	p.Ala467=	synonymous_variant	10/12	ENST00000382409.4	NP_066288.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DEAF1	ENST00000382409.4 linkuse as main transcript	c.1401G>A	p.Ala467=	synonymous_variant	10/12	1	NM_021008.4	ENSP00000371846	P1	O75398-1
	ENST00000527799.1 linkuse as main transcript	n.843+379C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes

AF:

0.0144

AC:

2198

AN:

152208

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00439

Gnomad AMI

AF:

0.00219

Gnomad AMR

AF:

0.0181

Gnomad ASJ

AF:

0.0421

Gnomad EAS

AF:

0.0152

Gnomad SAS

AF:

0.0550

Gnomad FIN

AF:

0.00226

Gnomad MID

AF:

0.0285

Gnomad NFE

AF:

0.0170

Gnomad OTH

AF:

0.0258

GnomAD3 exomes

AF:

0.0208

AC:

5240

AN:

251460

Hom.:

116

AF XY:

0.0244

AC XY:

3318

AN XY:

135906

show subpopulations

Gnomad AFR exome

AF:

0.00369

Gnomad AMR exome

AF:

0.0120

Gnomad ASJ exome

AF:

0.0428

Gnomad EAS exome

AF:

0.0158

Gnomad SAS exome

AF:

0.0652

Gnomad FIN exome

AF:

0.00264

Gnomad NFE exome

AF:

0.0162

Gnomad OTH exome

AF:

0.0235

GnomAD4 exome

AF:

0.0193

AC:

28244

AN:

1461812

Hom.:

502

Cov.:

AF XY:

0.0210

AC XY:

15238

AN XY:

727212

show subpopulations

Gnomad4 AFR exome

AF:

0.00394

Gnomad4 AMR exome

AF:

0.0133

Gnomad4 ASJ exome

AF:

0.0394

Gnomad4 EAS exome

AF:

0.00831

Gnomad4 SAS exome

AF:

0.0656

Gnomad4 FIN exome

AF:

0.00279

Gnomad4 NFE exome

AF:

0.0168

Gnomad4 OTH exome

AF:

0.0231

GnomAD4 genome

AF:

0.0144

AC:

2196

AN:

152326

Hom.:

Cov.:

AF XY:

0.0146

AC XY:

1090

AN XY:

74496

show subpopulations

Gnomad4 AFR

AF:

0.00440

Gnomad4 AMR

AF:

0.0180

Gnomad4 ASJ

AF:

0.0421

Gnomad4 EAS

AF:

0.0152

Gnomad4 SAS

AF:

0.0547

Gnomad4 FIN

AF:

0.00226

Gnomad4 NFE

AF:

0.0171

Gnomad4 OTH

AF:

0.0256

Alfa

AF:

0.0170

Hom.:

Bravo

AF:

0.0145

Asia WGS

AF:

0.0270

AC:

AN:

3478

EpiCase

AF:

0.0179

EpiControl

AF:

0.0188

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:4

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Feb 01, 2024	- -
Benign, criteria provided, single submitter	clinical testing	Athena Diagnostics	Sep 29, 2017	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 18, 2021	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.69

CADD

Benign

0.093

DANN

Benign

0.81

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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