7-112475603-C-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• 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
• Publications: 27 publications found

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]

IFRD1 Gene-Disease associations (from GenCC):

• spinocerebellar ataxia type 18

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

ENSG00000288640 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.51 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001550.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IFRD1	NM_001550.4	MANE Select	c.*84C>T		3_prime_UTR	Exon 12 of 12	NP_001541.2	O00458-1
	IFRD1	NM_001007245.3		c.*84C>T		3_prime_UTR	Exon 13 of 13	NP_001007246.1	O00458-1
	IFRD1	NM_001197079.2		c.*84C>T		3_prime_UTR	Exon 12 of 12	NP_001184008.1	O00458-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IFRD1	ENST00000403825.8	TSL:1 MANE Select	c.*84C>T		3_prime_UTR	Exon 12 of 12	ENSP00000384477.3	O00458-1
	IFRD1	ENST00000489994.5	TSL:1	n.1138C>T		non_coding_transcript_exon	Exon 4 of 4
	ENSG00000288640	ENST00000676282.1		n.*84C>T		non_coding_transcript_exon	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

African (AFR) AF: 0.425 AC: 7179 AN: 16906

American (AMR) AF: 0.391 AC: 12879 AN: 32964

Ashkenazi Jewish (ASJ) AF: 0.517 AC: 10596 AN: 20492

East Asian (EAS) AF: 0.122 AC: 3963 AN: 32358

South Asian (SAS) AF: 0.430 AC: 26451 AN: 61462

European-Finnish (FIN) AF: 0.469 AC: 16694 AN: 35584

Middle Eastern (MID) AF: 0.423 AC: 1226 AN: 2896

European-Non Finnish (NFE) AF: 0.514 AC: 216682 AN: 421568

Other (OTH) AF: 0.473 AC: 15837 AN: 33452

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

African (AFR) AF: 0.432 AC: 17884 AN: 41362

American (AMR) AF: 0.437 AC: 6674 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.533 AC: 1847 AN: 3468

East Asian (EAS) AF: 0.145 AC: 747 AN: 5160

South Asian (SAS) AF: 0.426 AC: 2049 AN: 4812

European-Finnish (FIN) AF: 0.456 AC: 4791 AN: 10506

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.515 AC: 34956 AN: 67900

Other (OTH) AF: 0.471 AC: 992 AN: 2104

Alfa AF: 0.481 Hom.: 19662

Bravo AF: 0.459

Asia WGS AF: 0.339 AC: 1179 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	8.4
DANN	Benign	0.58
PhyloP100		-0.19
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs7817; hg19: chr7-112115658;