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GeneBe

7-112450727-T-C

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_ModerateBP6_ModerateBP7

The NM_001550.4(IFRD1):c.39T>C(p.Gly13=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00048 in 1,612,072 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0024 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00028 ( 4 hom. )

Consequence

IFRD1
NM_001550.4 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.216
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]

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -5 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.41).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 7-112450727-T-C is Benign according to our data. Variant chr7-112450727-T-C is described in ClinVar as [Benign]. Clinvar id is 774131.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-0.216 with no splicing effect.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
IFRD1NM_001550.4 linkuse as main transcriptc.39T>C p.Gly13= synonymous_variant 1/12 ENST00000403825.8
IFRD1NM_001007245.3 linkuse as main transcriptc.39T>C p.Gly13= synonymous_variant 2/13
IFRD1NM_001197080.2 linkuse as main transcriptc.-56-5036T>C intron_variant
IFRD1NR_120333.1 linkuse as main transcriptn.220T>C non_coding_transcript_exon_variant 1/12

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
IFRD1ENST00000403825.8 linkuse as main transcriptc.39T>C p.Gly13= synonymous_variant 1/121 NM_001550.4 P3O00458-1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00239
AC:
364
AN:
152010
Hom.:
0
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.00821
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000720
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000208
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00316
Gnomad NFE
AF:
0.0000736
Gnomad OTH
AF:
0.00287
GnomAD3 exomes
AF:
0.000614
AC:
151
AN:
246116
Hom.:
1
AF XY:
0.000417
AC XY:
56
AN XY:
134452
show subpopulations
Gnomad AFR exome
AF:
0.00855
Gnomad AMR exome
AF:
0.000348
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0000327
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000544
Gnomad OTH exome
AF:
0.000331
GnomAD4 exome
AF:
0.000279
AC:
408
AN:
1459944
Hom.:
4
Cov.:
31
AF XY:
0.000238
AC XY:
173
AN XY:
726350
show subpopulations
Gnomad4 AFR exome
AF:
0.00825
Gnomad4 AMR exome
AF:
0.000514
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000580
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000369
Gnomad4 OTH exome
AF:
0.000862
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00240
AC:
365
AN:
152128
Hom.:
0
Cov.:
33
AF XY:
0.00227
AC XY:
169
AN XY:
74400
show subpopulations
Gnomad4 AFR
AF:
0.00821
Gnomad4 AMR
AF:
0.000719
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000208
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000736
Gnomad4 OTH
AF:
0.00284
Alfa
AF:
0.00103
Hom.:
0
Bravo
AF:
0.00276
Asia WGS
AF:
0.00173
AC:
6
AN:
3478
EpiCase
AF:
0.0000545
EpiControl
AF:
0.0000593

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeMar 30, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.41
Cadd
Benign
12
Dann
Benign
0.75
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.

Other links and lift over

dbSNP: rs140173633; hg19: chr7-112090782; API