chr19-43594045-A-G

Variant names:

• chr19-43594045-A-G
• rs427115
• NM_001007561.3:c.531-678T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001007561.3(IRGQ):​c.531-678T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.704 in 152,168 control chromosomes in the GnomAD database, including 38,032 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 0.70 (38032 hom., cov: 33)
• Consequence: IRGQ NM_001007561.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.79
• Publications: 10 publications found

Genes affected

IRGQ (HGNC:24868): (immunity related GTPase Q) Predicted to enable GTP binding activity. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.775 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001007561.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IRGQ	NM_001007561.3	MANE Select	c.531-678T>C		intron	N/A	NP_001007562.1
	IRGQ	NM_001388309.1		c.531-678T>C		intron	N/A	NP_001375238.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IRGQ	ENST00000422989.6	TSL:5 MANE Select	c.531-678T>C		intron	N/A	ENSP00000387535.1
	IRGQ	ENST00000602269.2	TSL:1	c.531-678T>C		intron	N/A	ENSP00000472250.1

Frequencies

GnomAD3 genomes AF: 0.704 AC: 106981 AN: 152048 Hom.: 37989 Cov.: 33

Gnomad AFR AF: 0.782

Gnomad AMI AF: 0.662

Gnomad AMR AF: 0.712

Gnomad ASJ AF: 0.728

Gnomad EAS AF: 0.640

Gnomad SAS AF: 0.634

Gnomad FIN AF: 0.603

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.679

Gnomad OTH AF: 0.698

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

GnomAD4 genome AF: 0.704 AC: 107076 AN: 152168 Hom.: 38032 Cov.: 33 AF XY: 0.696 AC XY: 51798 AN XY: 74394

African (AFR) AF: 0.782 AC: 32457 AN: 41516

American (AMR) AF: 0.712 AC: 10885 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.728 AC: 2525 AN: 3468

East Asian (EAS) AF: 0.639 AC: 3307 AN: 5172

South Asian (SAS) AF: 0.634 AC: 3061 AN: 4828

European-Finnish (FIN) AF: 0.603 AC: 6379 AN: 10576

Middle Eastern (MID) AF: 0.636 AC: 187 AN: 294

European-Non Finnish (NFE) AF: 0.679 AC: 46199 AN: 67998

Other (OTH) AF: 0.696 AC: 1472 AN: 2114

Alfa AF: 0.692 Hom.: 8117

Bravo AF: 0.718

Asia WGS AF: 0.633 AC: 2199 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.072
DANN	Benign	0.33
PhyloP100		-2.8
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs427115; hg19: chr19-44098197;