rs728273

chr7-112428046-G-C

Variant summary

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

The ENST00000005558.8(IFRD1):c.-182+4614G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.513 in 151,968 control chromosomes in the GnomAD database, including 21,363 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 0.51 (21363 hom., cov: 32)
• Consequence: IFRD1 ENST00000005558.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.288

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]

LOC105375457 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.619 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375457	XR_001745325.2	n.5968C>G		non_coding_transcript_exon_variant	3/3
IFRD1	NM_001007245.3	c.-182+4614G>C		intron_variant
IFRD1	NM_001197080.2	c.-57+4614G>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IFRD1	ENST00000005558.8	c.-182+4614G>C		intron_variant		1		P3
IFRD1	ENST00000432734.1	c.-182+4614G>C		intron_variant		4
IFRD1	ENST00000621379.4	c.-57+4614G>C		intron_variant		2		A1
IFRD1	ENST00000675578.1	c.-112+4614G>C		intron_variant				P3

Frequencies

GnomAD3 genomes AF: 0.513 AC: 77947 AN: 151848 Hom.: 21360 Cov.: 32

Gnomad AFR AF: 0.321

Gnomad AMI AF: 0.491

Gnomad AMR AF: 0.508

Gnomad ASJ AF: 0.516

Gnomad EAS AF: 0.637

Gnomad SAS AF: 0.435

Gnomad FIN AF: 0.679

Gnomad MID AF: 0.353

Gnomad NFE AF: 0.603

Gnomad OTH AF: 0.501

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

GnomAD4 genome AF: 0.513 AC: 77961 AN: 151968 Hom.: 21363 Cov.: 32 AF XY: 0.515 AC XY: 38286 AN XY: 74290

Gnomad4 AFR AF: 0.320

Gnomad4 AMR AF: 0.508

Gnomad4 ASJ AF: 0.516

Gnomad4 EAS AF: 0.638

Gnomad4 SAS AF: 0.436

Gnomad4 FIN AF: 0.679

Gnomad4 NFE AF: 0.603

Gnomad4 OTH AF: 0.497

Alfa AF: 0.575 Hom.: 3242

Bravo AF: 0.492

Asia WGS AF: 0.473 AC: 1641 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.84
Dann	Benign	0.37

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: rs728273; hg19: chr7-112068101;