7-112475603-C-T

Variant names:

• chr7-112475603-C-T
• rs7817
• NM_001550.4:c.*84C>T

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP6 BA1

The NM_001550.4(IFRD1):​c.*84C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.472 in 809,472 control chromosomes in the GnomAD database, including 93,673 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in Lovd as Benign (no stars).

• Frequency:
  • Genomes: 𝑓 0.46 (16792 hom., cov: 32)
  • Exomes 𝑓: 0.47 (76881 hom.)
• Consequence: IFRD1 NM_001550.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.189

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 -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BP6: Variant 7-112475603-C-T is Benign according to our data. Variant chr7-112475603-C-T is described in Lovd as [Benign].
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.51 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IFRD1	NM_001550.4	c.*84C>T		3_prime_UTR_variant	Exon 12 of 12	ENST00000403825.8	NP_001541.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IFRD1	ENST00000403825.8	c.*84C>T		3_prime_UTR_variant	Exon 12 of 12	1	NM_001550.4	ENSP00000384477.3
ENSG00000288640	ENST00000676282.1	n.*84C>T		non_coding_transcript_exon_variant	Exon 12 of 15			ENSP00000501830.1
ENSG00000288640	ENST00000676282.1	n.*84C>T		3_prime_UTR_variant	Exon 12 of 15			ENSP00000501830.1

Frequencies

GnomAD3 genomes AF: 0.464 AC: 70442 AN: 151672 Hom.: 16790 Cov.: 32

Gnomad AFR AF: 0.433

Gnomad AMI AF: 0.448

Gnomad AMR AF: 0.438

Gnomad ASJ AF: 0.533

Gnomad EAS AF: 0.145

Gnomad SAS AF: 0.426

Gnomad FIN AF: 0.456

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.515

Gnomad OTH AF: 0.471

GnomAD4 exome AF: 0.474 AC: 311507 AN: 657682 Hom.: 76881 Cov.: 9 AF XY: 0.474 AC XY: 165774 AN XY: 349942

Gnomad4 AFR exome AF: 0.425

Gnomad4 AMR exome AF: 0.391

Gnomad4 ASJ exome AF: 0.517

Gnomad4 EAS exome AF: 0.122

Gnomad4 SAS exome AF: 0.430

Gnomad4 FIN exome AF: 0.469

Gnomad4 NFE exome AF: 0.514

Gnomad4 OTH exome AF: 0.473

GnomAD4 genome AF: 0.464 AC: 70468 AN: 151790 Hom.: 16792 Cov.: 32 AF XY: 0.459 AC XY: 34062 AN XY: 74170

Gnomad4 AFR AF: 0.432

Gnomad4 AMR AF: 0.437

Gnomad4 ASJ AF: 0.533

Gnomad4 EAS AF: 0.145

Gnomad4 SAS AF: 0.426

Gnomad4 FIN AF: 0.456

Gnomad4 NFE AF: 0.515

Gnomad4 OTH AF: 0.471

Alfa AF: 0.482 Hom.: 14377

Bravo AF: 0.459

Asia WGS AF: 0.339 AC: 1179 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	8.4
DANN	Benign	0.58

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs7817; hg19: chr7-112115658;