7-112461852-ATTTT-ATTT

Variant names:

• chr7-112461852-AT-A
• rs61603869
• NM_001550.4:c.568-3delT

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6 BA1

The NM_001550.4(IFRD1):​c.568-3delT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0935 in 1,161,746 control chromosomes in the GnomAD database, including 3,450 homozygotes. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in Lovd as Benign (no stars).

• Frequency:
  • Genomes: 𝑓 0.094 (802 hom., cov: 27)
  • Exomes 𝑓: 0.093 (2648 hom.)
• Consequence: IFRD1 NM_001550.4 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.209

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 -9 ACMG points.

• BP6: Variant 7-112461852-AT-A is Benign according to our data. Variant chr7-112461852-AT-A is described in Lovd as [Benign]. Variant chr7-112461852-AT-A is described in Lovd as [Likely_benign].
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.157 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IFRD1	NM_001550.4	c.568-3delT		splice_region_variant, intron_variant	Intron 5 of 11	ENST00000403825.8	NP_001541.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IFRD1	ENST00000403825.8	c.568-3delT		splice_region_variant, intron_variant	Intron 5 of 11	1	NM_001550.4	ENSP00000384477.3
ENSG00000288640	ENST00000676282.1	n.568-3delT		splice_region_variant, intron_variant	Intron 5 of 14			ENSP00000501830.1

Frequencies

GnomAD3 genomes AF: 0.0939 AC: 14056 AN: 149702 Hom.: 800 Cov.: 27

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.0736

Gnomad AMR AF: 0.0585

Gnomad ASJ AF: 0.0747

Gnomad EAS AF: 0.0752

Gnomad SAS AF: 0.0967

Gnomad FIN AF: 0.0354

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0729

Gnomad OTH AF: 0.0864

GnomAD3 exomes AF: 0.101 AC: 15478 AN: 153706 Hom.: 493 AF XY: 0.103 AC XY: 8654 AN XY: 83692

Gnomad AFR exome AF: 0.192

Gnomad AMR exome AF: 0.0566

Gnomad ASJ exome AF: 0.0917

Gnomad EAS exome AF: 0.133

Gnomad SAS exome AF: 0.126

Gnomad FIN exome AF: 0.0479

Gnomad NFE exome AF: 0.103

Gnomad OTH exome AF: 0.0844

GnomAD4 exome AF: 0.0934 AC: 94559 AN: 1011950 Hom.: 2648 Cov.: 8 AF XY: 0.0935 AC XY: 48050 AN XY: 513844

Gnomad4 AFR exome AF: 0.173

Gnomad4 AMR exome AF: 0.0501

Gnomad4 ASJ exome AF: 0.0831

Gnomad4 EAS exome AF: 0.101

Gnomad4 SAS exome AF: 0.115

Gnomad4 FIN exome AF: 0.0466

Gnomad4 NFE exome AF: 0.0935

Gnomad4 OTH exome AF: 0.100

GnomAD4 genome AF: 0.0939 AC: 14073 AN: 149796 Hom.: 802 Cov.: 27 AF XY: 0.0915 AC XY: 6685 AN XY: 73092

Gnomad4 AFR AF: 0.161

Gnomad4 AMR AF: 0.0583

Gnomad4 ASJ AF: 0.0747

Gnomad4 EAS AF: 0.0752

Gnomad4 SAS AF: 0.0967

Gnomad4 FIN AF: 0.0354

Gnomad4 NFE AF: 0.0729

Gnomad4 OTH AF: 0.0855

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs61603869; hg19: chr7-112101907;