7-112465699-G-T

Variant names:

• chr7-112465699-G-T
• rs3807213
• NM_001550.4:c.907-2282G>T

Variant summary

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

The NM_001550.4(IFRD1):​c.907-2282G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.561 in 151,948 control chromosomes in the GnomAD database, including 24,615 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 0.56 (24615 hom., cov: 32)
• Consequence: IFRD1 NM_001550.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.213

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.598 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IFRD1	NM_001550.4	c.907-2282G>T		intron_variant	Intron 8 of 11	ENST00000403825.8	NP_001541.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IFRD1	ENST00000403825.8	c.907-2282G>T		intron_variant	Intron 8 of 11	1	NM_001550.4	ENSP00000384477.3
ENSG00000288640	ENST00000676282.1	n.907-2282G>T		intron_variant	Intron 8 of 14			ENSP00000501830.1

Frequencies

GnomAD3 genomes AF: 0.561 AC: 85204 AN: 151830 Hom.: 24601 Cov.: 32

Gnomad AFR AF: 0.604

Gnomad AMI AF: 0.468

Gnomad AMR AF: 0.501

Gnomad ASJ AF: 0.621

Gnomad EAS AF: 0.145

Gnomad SAS AF: 0.532

Gnomad FIN AF: 0.490

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.592

Gnomad OTH AF: 0.559

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

GnomAD4 genome AF: 0.561 AC: 85258 AN: 151948 Hom.: 24615 Cov.: 32 AF XY: 0.553 AC XY: 41055 AN XY: 74258

Gnomad4 AFR AF: 0.604

Gnomad4 AMR AF: 0.500

Gnomad4 ASJ AF: 0.621

Gnomad4 EAS AF: 0.145

Gnomad4 SAS AF: 0.532

Gnomad4 FIN AF: 0.490

Gnomad4 NFE AF: 0.592

Gnomad4 OTH AF: 0.558

Alfa AF: 0.575 Hom.: 32489

Bravo AF: 0.560

Asia WGS AF: 0.387 AC: 1350 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.7
DANN	Benign	0.62
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs3807213; hg19: chr7-112105754;