Variant chr7-112462300-T-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_001550.4(IFRD1):c.828T>G(p.Ser276=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.236 in 1,611,978 control chromosomes in the GnomAD database, including 46,144 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.26 ( 5469 hom., cov: 32)

Exomes 𝑓: 0.23 ( 40675 hom. )

Consequence

IFRD1
NM_001550.4 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:3

Conservation

PhyloP100: 1.56

Variant links:

Genes affected

IFRD1 (HGNC:5456): (interferon related developmental regulator 1) This gene is an immediate early gene that encodes a protein related to interferon-gamma. This protein may function as a transcriptional co-activator/repressor that controls the growth and differentiation of specific cell types during embryonic development and tissue regeneration. Mutations in this gene are associated with sensory/motor neuropathy with ataxia. This gene may also be involved in modulating the pathogenesis of cystic fibrosis lung disease. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Oct 2010]

IFRD1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.51).

BP6

Variant 7-112462300-T-G is Benign according to our data. Variant chr7-112462300-T-G is described in ClinVar as [Benign]. Clinvar id is 1284350.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr7-112462300-T-G is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=1.56 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.323 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IFRD1	NM_001550.4 linkuse as main transcript	c.828T>G	p.Ser276=	synonymous_variant	8/12	ENST00000403825.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IFRD1	ENST00000403825.8 linkuse as main transcript	c.828T>G	p.Ser276=	synonymous_variant	8/12	1	NM_001550.4	P3	O00458-1

Frequencies

GnomAD3 genomes

AF:

0.263

AC:

39902

AN:

152006

Hom.:

5467

Cov.:

show subpopulations

Gnomad AFR

AF:

0.328

Gnomad AMI

AF:

0.385

Gnomad AMR

AF:

0.207

Gnomad ASJ

AF:

0.258

Gnomad EAS

AF:

0.196

Gnomad SAS

AF:

0.202

Gnomad FIN

AF:

0.290

Gnomad MID

AF:

0.443

Gnomad NFE

AF:

0.238

Gnomad OTH

AF:

0.271

GnomAD3 exomes

AF:

0.236

AC:

59166

AN:

251074

Hom.:

7249

AF XY:

0.235

AC XY:

31852

AN XY:

135688

show subpopulations

Gnomad AFR exome

AF:

0.332

Gnomad AMR exome

AF:

0.172

Gnomad ASJ exome

AF:

0.277

Gnomad EAS exome

AF:

0.192

Gnomad SAS exome

AF:

0.203

Gnomad FIN exome

AF:

0.292

Gnomad NFE exome

AF:

0.241

Gnomad OTH exome

AF:

0.257

GnomAD4 exome

AF:

0.233

AC:

340702

AN:

1459854

Hom.:

40675

Cov.:

AF XY:

0.233

AC XY:

169008

AN XY:

726346

show subpopulations

Gnomad4 AFR exome

AF:

0.336

Gnomad4 AMR exome

AF:

0.178

Gnomad4 ASJ exome

AF:

0.271

Gnomad4 EAS exome

AF:

0.181

Gnomad4 SAS exome

AF:

0.204

Gnomad4 FIN exome

AF:

0.286

Gnomad4 NFE exome

AF:

0.232

Gnomad4 OTH exome

AF:

0.243

GnomAD4 genome

AF:

0.263

AC:

39935

AN:

152124

Hom.:

5469

Cov.:

AF XY:

0.261

AC XY:

19375

AN XY:

74334

show subpopulations

Gnomad4 AFR

AF:

0.328

Gnomad4 AMR

AF:

0.207

Gnomad4 ASJ

AF:

0.258

Gnomad4 EAS

AF:

0.196

Gnomad4 SAS

AF:

0.201

Gnomad4 FIN

AF:

0.290

Gnomad4 NFE

AF:

0.238

Gnomad4 OTH

AF:

0.269

Alfa

AF:

0.243

Hom.:

9205

Bravo

AF:

0.261

Asia WGS

AF:

0.216

AC:

752

AN:

3478

EpiCase

AF:

0.246

EpiControl

AF:

0.248

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Benign:2

Benign, no assertion criteria provided	clinical testing	Clinical Genetics, Academic Medical Center	-	- -
Benign, no assertion criteria provided	clinical testing	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	-	- -

not provided

Benign:1

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

-0.51

CADD

Benign

9.1

DANN

Benign

0.83

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