Variant rs10902188 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.1512C>T(p.Cys504Cys) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0888 in 1,612,784 control chromosomes in the GnomAD database, including 7,246 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.086 ( 670 hom., cov: 30)

Exomes 𝑓: 0.089 ( 6576 hom. )

Consequence

DEAF1
NM_021008.4 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.625

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:

DEAF1 (HGNC:):

DEAF1 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=-0.49).

BP6

Variant 11-654043-G-A is Benign according to our data. Variant chr11-654043-G-A is described in ClinVar as [Benign]. Clinvar id is 585773.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.625 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.177 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.1512C>T	p.Cys504Cys	synonymous_variant	11/12	ENST00000382409.4	NP_066288.2	O75398-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DEAF1	ENST00000382409.4 linkuse as main transcript	c.1512C>T	p.Cys504Cys	synonymous_variant	11/12	1	NM_021008.4	ENSP00000371846.3		O75398-1

Frequencies

GnomAD3 genomes

AF:

0.0858

AC:

13036

AN:

151894

Hom.:

665

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0549

Gnomad AMI

AF:

0.0680

Gnomad AMR

AF:

0.183

Gnomad ASJ

AF:

0.0724

Gnomad EAS

AF:

0.153

Gnomad SAS

AF:

0.0833

Gnomad FIN

AF:

0.0488

Gnomad MID

AF:

0.0886

Gnomad NFE

AF:

0.0849

Gnomad OTH

AF:

0.0750

GnomAD3 exomes

AF:

0.103

AC:

25780

AN:

249718

Hom.:

1786

AF XY:

0.0975

AC XY:

13183

AN XY:

135180

show subpopulations

Gnomad AFR exome

AF:

0.0541

Gnomad AMR exome

AF:

0.221

Gnomad ASJ exome

AF:

0.0798

Gnomad EAS exome

AF:

0.157

Gnomad SAS exome

AF:

0.0809

Gnomad FIN exome

AF:

0.0527

Gnomad NFE exome

AF:

0.0837

Gnomad OTH exome

AF:

0.0920

GnomAD4 exome

AF:

0.0891

AC:

130118

AN:

1460776

Hom.:

6576

Cov.:

AF XY:

0.0883

AC XY:

64180

AN XY:

726688

show subpopulations

Gnomad4 AFR exome

AF:

0.0545

Gnomad4 AMR exome

AF:

0.216

Gnomad4 ASJ exome

AF:

0.0796

Gnomad4 EAS exome

AF:

0.158

Gnomad4 SAS exome

AF:

0.0774

Gnomad4 FIN exome

AF:

0.0519

Gnomad4 NFE exome

AF:

0.0855

Gnomad4 OTH exome

AF:

0.0875

GnomAD4 genome

AF:

0.0859

AC:

13059

AN:

152008

Hom.:

670

Cov.:

AF XY:

0.0879

AC XY:

6528

AN XY:

74300

show subpopulations

Gnomad4 AFR

AF:

0.0550

Gnomad4 AMR

AF:

0.183

Gnomad4 ASJ

AF:

0.0724

Gnomad4 EAS

AF:

0.154

Gnomad4 SAS

AF:

0.0834

Gnomad4 FIN

AF:

0.0488

Gnomad4 NFE

AF:

0.0849

Gnomad4 OTH

AF:

0.0794

Alfa

AF:

0.0849

Hom.:

888

Bravo

AF:

0.0939

Asia WGS

AF:

0.148

AC:

514

AN:

3478

EpiCase

AF:

0.0832

EpiControl

AF:

0.0883

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

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.49

CADD

Benign

0.83

DANN

Benign

0.71

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.9

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

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