7-112462104-A-C

Variant names:

• chr7-112462104-A-C
• rs1354426179
• NM_001550.4:c.722A>C

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001550.4(IFRD1):​c.722A>C​(p.His241Pro) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: IFRD1 NM_001550.4 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 7.04

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 Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IFRD1	NM_001550.4	c.722A>C	p.His241Pro	missense_variant	Exon 7 of 12	ENST00000403825.8	NP_001541.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IFRD1	ENST00000403825.8	c.722A>C	p.His241Pro	missense_variant	Exon 7 of 12	1	NM_001550.4	ENSP00000384477.3
ENSG00000288640	ENST00000676282.1	n.722A>C		non_coding_transcript_exon_variant	Exon 7 of 15			ENSP00000501830.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 32

Bravo AF: 0.00000756

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Apr 07, 2022

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.722A>C (p.H241P) alteration is located in exon 7 (coding exon 7) of the IFRD1 gene. This alteration results from a A to C substitution at nucleotide position 722, causing the histidine (H) at amino acid position 241 to be replaced by a proline (P). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.10
BayesDel_addAF	Pathogenic	0.18	D
BayesDel_noAF	Uncertain	0.020
CADD	Benign	23
DANN	Benign	0.97
DEOGEN2	Uncertain	0.59	D;.;D;.
Eigen	Benign	0.076
Eigen_PC	Benign	0.18
FATHMM_MKL	Uncertain	0.96	D
LIST_S2	Benign	0.62	.;.;T;T
M_CAP	Benign	0.033	D
MetaRNN	Uncertain	0.68	D;D;D;D
MetaSVM	Benign	-0.65	T
MutationAssessor	Uncertain	2.3	M;.;M;.
PrimateAI	Uncertain	0.55	T
PROVEAN	Pathogenic	-8.5	D;.;D;D
REVEL	Uncertain	0.39
Sift	Uncertain	0.018	D;.;D;D
Sift4G	Uncertain	0.027	D;D;D;D
Polyphen		0.0030	B;.;B;.
Vest4		0.55
MutPred		0.70		Gain of loop (P = 0.0166);.;Gain of loop (P = 0.0166);.;
MVP		0.69
MPC		0.70
ClinPred		0.99	D
GERP RS		4.4
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Varity_R		0.90
gMVP		0.85

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.15		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: rs1354426179; hg19: chr7-112102159;