7-112454688-A-G

Position:

• chr7-112454688-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001550.4(IFRD1):​c.95-1075A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0709 in 152,114 control chromosomes in the GnomAD database, including 548 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 0.071 (548 hom., cov: 32)
• Consequence: IFRD1 NM_001550.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.486

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]

ENSG00000288640 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.198 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IFRD1	NM_001550.4	c.95-1075A>G		intron_variant		ENST00000403825.8	NP_001541.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IFRD1	ENST00000403825.8	c.95-1075A>G		intron_variant		1	NM_001550.4	ENSP00000384477.3
ENSG00000288640	ENST00000676282.1	n.95-1075A>G		intron_variant				ENSP00000501830.1

Frequencies

GnomAD3 genomes AF: 0.0709 AC: 10779 AN: 151996 Hom.: 546 Cov.: 32

Gnomad AFR AF: 0.0391

Gnomad AMI AF: 0.0833

Gnomad AMR AF: 0.135

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.0725

Gnomad SAS AF: 0.208

Gnomad FIN AF: 0.0686

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0618

Gnomad OTH AF: 0.0813

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0709 AC: 10784 AN: 152114 Hom.: 548 Cov.: 32 AF XY: 0.0754 AC XY: 5607 AN XY: 74382

Gnomad4 AFR AF: 0.0390

Gnomad4 AMR AF: 0.135

Gnomad4 ASJ AF: 0.149

Gnomad4 EAS AF: 0.0723

Gnomad4 SAS AF: 0.208

Gnomad4 FIN AF: 0.0686

Gnomad4 NFE AF: 0.0618

Gnomad4 OTH AF: 0.0862

Alfa AF: 0.0727 Hom.: 735

Bravo AF: 0.0719

Asia WGS AF: 0.185 AC: 642 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.3
DANN	Benign	0.85

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

Other links and lift over

dbSNP: rs6956741; hg19: chr7-112094743;