rs17159640

chr7-112446278-A-T

Variant summary

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

The ENST00000005558.8(IFRD1):c.-181-4230A>T variant causes a intron change. The variant allele was found at a frequency of 0.0632 in 221,618 control chromosomes in the GnomAD database, including 625 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 0.062 (386 hom., cov: 33)
  • Exomes 𝑓: 0.065 (239 hom.)
• Consequence: IFRD1 ENST00000005558.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 7.01

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.54).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.133 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IFRD1	NM_001007245.3	c.-181-4230A>T		intron_variant
IFRD1	NM_001197080.2	c.-56-9485A>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000321498.5	n.98T>A		non_coding_transcript_exon_variant	1/1
	ENST00000676289.1	n.98T>A		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.0622 AC: 9465 AN: 152190 Hom.: 385 Cov.: 33

Gnomad AFR AF: 0.0636

Gnomad AMI AF: 0.0285

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.0744

Gnomad EAS AF: 0.0728

Gnomad SAS AF: 0.142

Gnomad FIN AF: 0.0246

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0449

Gnomad OTH AF: 0.0737

GnomAD4 exome AF: 0.0655 AC: 4539 AN: 69310 Hom.: 239 Cov.: 0 AF XY: 0.0628 AC XY: 2574 AN XY: 40990

Gnomad4 AFR exome AF: 0.0658

Gnomad4 AMR exome AF: 0.174

Gnomad4 ASJ exome AF: 0.0671

Gnomad4 EAS exome AF: 0.0800

Gnomad4 SAS exome AF: 0.105

Gnomad4 FIN exome AF: 0.0192

Gnomad4 NFE exome AF: 0.0369

Gnomad4 OTH exome AF: 0.0420

GnomAD4 genome AF: 0.0622 AC: 9478 AN: 152308 Hom.: 386 Cov.: 33 AF XY: 0.0646 AC XY: 4812 AN XY: 74480

Gnomad4 AFR AF: 0.0637

Gnomad4 AMR AF: 0.130

Gnomad4 ASJ AF: 0.0744

Gnomad4 EAS AF: 0.0722

Gnomad4 SAS AF: 0.142

Gnomad4 FIN AF: 0.0246

Gnomad4 NFE AF: 0.0450

Gnomad4 OTH AF: 0.0772

Alfa AF: 0.0499 Hom.: 28

Bravo AF: 0.0693

Asia WGS AF: 0.138 AC: 478 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
Cadd	Benign	9.8
Dann	Benign	0.67

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: rs17159640; hg19: chr7-112086333;