Variant rs6968084 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001550.4(IFRD1):c.409+28C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.152 in 1,606,626 control chromosomes in the GnomAD database, including 20,669 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.16 ( 2197 hom., cov: 32)

Exomes 𝑓: 0.15 ( 18472 hom. )

Consequence

IFRD1
NM_001550.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0110

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:

ENSG00000288640 (HGNC:):

ENSG00000288640 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0034398139).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.292 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IFRD1	NM_001550.4 link	c.409+28C>T		intron_variant		ENST00000403825.8	NP_001541.2	O00458-1A4D0U1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IFRD1	ENST00000403825.8 link	c.409+28C>T		intron_variant		1	NM_001550.4	ENSP00000384477.3		O00458-1
ENSG00000288640	ENST00000676282.1 link	n.409+28C>T		intron_variant				ENSP00000501830.1

Frequencies

GnomAD3 genomes

AF:

0.164

AC:

24860

AN:

151952

Hom.:

2195

Cov.:

show subpopulations

Gnomad AFR

AF:

0.198

Gnomad AMI

AF:

0.158

Gnomad AMR

AF:

0.192

Gnomad ASJ

AF:

0.225

Gnomad EAS

AF:

0.143

Gnomad SAS

AF:

0.305

Gnomad FIN

AF:

0.103

Gnomad MID

AF:

0.136

Gnomad NFE

AF:

0.134

Gnomad OTH

AF:

0.164

GnomAD3 exomes

AF:

0.174

AC:

43694

AN:

250674

Hom.:

4404

AF XY:

0.178

AC XY:

24101

AN XY:

135580

show subpopulations

Gnomad AFR exome

AF:

0.198

Gnomad AMR exome

AF:

0.223

Gnomad ASJ exome

AF:

0.230

Gnomad EAS exome

AF:

0.144

Gnomad SAS exome

AF:

0.306

Gnomad FIN exome

AF:

0.102

Gnomad NFE exome

AF:

0.135

Gnomad OTH exome

AF:

0.160

GnomAD4 exome

AF:

0.151

AC:

219220

AN:

1454558

Hom.:

18472

Cov.:

AF XY:

0.155

AC XY:

112396

AN XY:

724086

show subpopulations

Gnomad4 AFR exome

AF:

0.196

Gnomad4 AMR exome

AF:

0.215

Gnomad4 ASJ exome

AF:

0.231

Gnomad4 EAS exome

AF:

0.126

Gnomad4 SAS exome

AF:

0.297

Gnomad4 FIN exome

AF:

0.102

Gnomad4 NFE exome

AF:

0.135

Gnomad4 OTH exome

AF:

0.171

GnomAD4 genome

AF:

0.164

AC:

24881

AN:

152068

Hom.:

2197

Cov.:

AF XY:

0.166

AC XY:

12302

AN XY:

74330

show subpopulations

Gnomad4 AFR

AF:

0.198

Gnomad4 AMR

AF:

0.192

Gnomad4 ASJ

AF:

0.225

Gnomad4 EAS

AF:

0.143

Gnomad4 SAS

AF:

0.305

Gnomad4 FIN

AF:

0.103

Gnomad4 NFE

AF:

0.134

Gnomad4 OTH

AF:

0.168

Alfa

AF:

0.148

Hom.:

3988

Bravo

AF:

0.169

TwinsUK

AF:

0.130

AC:

483

ALSPAC

AF:

0.137

AC:

529

ESP6500AA

AF:

0.201

AC:

886

ESP6500EA

AF:

0.138

AC:

1189

ExAC

AF:

0.176

AC:

21364

Asia WGS

AF:

0.268

AC:

930

AN:

3478

EpiCase

AF:

0.140

EpiControl

AF:

0.143

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.65

BayesDel_noAF

Benign

-0.56

CADD

Benign

9.1

DANN

Benign

0.53

DEOGEN2

Benign

0.013

Eigen

Benign

-1.1

Eigen_PC

Benign

-1.2

FATHMM_MKL

Benign

0.046

LIST_S2

Benign

0.27

MetaRNN

Benign

0.0034

MetaSVM

Benign

-0.99

PROVEAN

Benign

-0.58

REVEL

Benign

0.0010

Sift

Pathogenic

0.0

Polyphen

0.058

Vest4

0.044

ClinPred

0.014

GERP RS

-1.3

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over