Variant 11-653968-T-C 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 NM_021008.4(DEAF1):c.1587A>G(p.Gln529=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.141 in 1,613,254 control chromosomes in the GnomAD database, including 23,850 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.24 ( 7249 hom., cov: 30)

Exomes 𝑓: 0.13 ( 16601 hom. )

Consequence

DEAF1
NM_021008.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 1.51

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.59).

BP6

Variant 11-653968-T-C is Benign according to our data. Variant chr11-653968-T-C is described in ClinVar as [Benign]. Clinvar id is 585774.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=1.51 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.545 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.1587A>G	p.Gln529=	synonymous_variant	11/12	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.1587A>G	p.Gln529=	synonymous_variant	11/12	1	NM_021008.4	ENSP00000371846	P1	O75398-1

Frequencies

GnomAD3 genomes

AF:

0.242

AC:

36648

AN:

151720

Hom.:

7231

Cov.:

show subpopulations

Gnomad AFR

AF:

0.551

Gnomad AMI

AF:

0.0530

Gnomad AMR

AF:

0.143

Gnomad ASJ

AF:

0.133

Gnomad EAS

AF:

0.209

Gnomad SAS

AF:

0.146

Gnomad FIN

AF:

0.0970

Gnomad MID

AF:

0.212

Gnomad NFE

AF:

0.116

Gnomad OTH

AF:

0.228

GnomAD3 exomes

AF:

0.150

AC:

37582

AN:

251242

Hom.:

4506

AF XY:

0.144

AC XY:

19609

AN XY:

135794

show subpopulations

Gnomad AFR exome

AF:

0.558

Gnomad AMR exome

AF:

0.0861

Gnomad ASJ exome

AF:

0.135

Gnomad EAS exome

AF:

0.228

Gnomad SAS exome

AF:

0.141

Gnomad FIN exome

AF:

0.0982

Gnomad NFE exome

AF:

0.112

Gnomad OTH exome

AF:

0.139

GnomAD4 exome

AF:

0.131

AC:

191242

AN:

1461416

Hom.:

16601

Cov.:

AF XY:

0.130

AC XY:

94627

AN XY:

726996

show subpopulations

Gnomad4 AFR exome

AF:

0.562

Gnomad4 AMR exome

AF:

0.0929

Gnomad4 ASJ exome

AF:

0.138

Gnomad4 EAS exome

AF:

0.201

Gnomad4 SAS exome

AF:

0.144

Gnomad4 FIN exome

AF:

0.101

Gnomad4 NFE exome

AF:

0.115

Gnomad4 OTH exome

AF:

0.162

GnomAD4 genome

AF:

0.242

AC:

36696

AN:

151838

Hom.:

7249

Cov.:

AF XY:

0.238

AC XY:

17667

AN XY:

74224

show subpopulations

Gnomad4 AFR

AF:

0.551

Gnomad4 AMR

AF:

0.143

Gnomad4 ASJ

AF:

0.133

Gnomad4 EAS

AF:

0.208

Gnomad4 SAS

AF:

0.146

Gnomad4 FIN

AF:

0.0970

Gnomad4 NFE

AF:

0.116

Gnomad4 OTH

AF:

0.227

Alfa

AF:

0.140

Hom.:

3506

Bravo

AF:

0.259

Asia WGS

AF:

0.209

AC:

728

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Athena Diagnostics	Apr 20, 2017	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Feb 01, 2024	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.59

CADD

Benign

DANN

Benign

0.63

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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