chr7-128937860-C-CGCGGGGCGGGGCGGG

Position:

• chr7-128937860-C-CGCGGGGCGGGGCGGG

Variant summary

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

The NM_001347928.2(IRF5):​c.-12+598_-12+612dup variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.00024 (0 hom., cov: 0)
  • Failed GnomAD Quality Control
• Consequence: IRF5 NM_001347928.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.213

Genes affected

IRF5 (HGNC:6120): (interferon regulatory factor 5) This gene encodes a member of the interferon regulatory factor (IRF) family, a group of transcription factors with diverse roles, including virus-mediated activation of interferon, and modulation of cell growth, differentiation, apoptosis, and immune system activity. Members of the IRF family are characterized by a conserved N-terminal DNA-binding domain containing tryptophan (W) repeats. Alternative promoter use and alternative splicing result in multiple transcript variants, and a 30-nt indel polymorphism (SNP rs60344245) can result in loss of a 10-aa segment. [provided by RefSeq, Dec 2016]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IRF5	NM_001347928.2	c.-12+598_-12+612dup		intron_variant			NP_001334857.1
IRF5	XM_011516160.2	c.-12+29_-12+43dup		intron_variant			XP_011514462.1
IRF5	XM_047420338.1	c.-12+29_-12+43dup		intron_variant			XP_047276294.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IRF5	ENST00000489702.6	c.-12+29_-12+43dup		intron_variant		5		ENSP00000418037
IRF5	ENST00000652525.1	c.-12+169_-12+183dup		intron_variant				ENSP00000498293
IRF5	ENST00000700148.1	n.52+29_52+43dup		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.00 AC: 36 AN: 149950 Hom.: 0 Cov.: 0 FAILED QC

Gnomad AFR AF: 0.0000976

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000398

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00321

Gnomad NFE AF: 0.000358

Gnomad OTH AF: 0.000486

GnomAD4 exome Cov.: 0

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.000240 AC: 36 AN: 149950 Hom.: 0 Cov.: 0 AF XY: 0.000246 AC XY: 18 AN XY: 73086

Gnomad4 AFR AF: 0.0000976

Gnomad4 AMR AF: 0.000398

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000358

Gnomad4 OTH AF: 0.000486

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs77571059; hg19: chr7-128577914;