Genetic Variant IRGQ:c.*1101T>C (chr19-43590925-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001007561.3(IRGQ):c.*1101T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.307 in 151,842 control chromosomes in the GnomAD database, including 7,589 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 0.31 ( 7583 hom., cov: 31)

Exomes 𝑓: 0.34 ( 6 hom. )

Consequence

IRGQ
NM_001007561.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.287

Publications

17 publications found

Variant links:

Genes affected

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

IRGQ links:

ENSG00000268361 (HGNC:):

ENSG00000268361 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.458 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IRGQ	NM_001007561.3	MANE Select	c.*1101T>C		3_prime_UTR	Exon 3 of 3	NP_001007562.1	Q8WZA9
	IRGQ	NM_001388309.1		c.*1101T>C		3_prime_UTR	Exon 3 of 3	NP_001375238.1	Q8WZA9

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
IRGQ	ENST00000422989.6	TSL:5 MANE Select	c.*1101T>C	3_prime_UTR	Exon 3 of 3	ENSP00000387535.1	Q8WZA9
IRGQ	ENST00000602269.2	TSL:1	c.*1101T>C	3_prime_UTR	Exon 2 of 2	ENSP00000472250.1	Q8WZA9
ENSG00000268361	ENST00000594374.1	TSL:3	c.168+1943T>C	intron	N/A	ENSP00000472698.1	M0R2N6

Frequencies

GnomAD3 genomes

AF:

0.307

AC:

46485

AN:

151658

Hom.:

7574

Cov.:

show subpopulations

Gnomad AFR

AF:

0.226

Gnomad AMI

AF:

0.302

Gnomad AMR

AF:

0.359

Gnomad ASJ

AF:

0.347

Gnomad EAS

AF:

0.474

Gnomad SAS

AF:

0.257

Gnomad FIN

AF:

0.365

Gnomad MID

AF:

0.239

Gnomad NFE

AF:

0.324

Gnomad OTH

AF:

0.307

GnomAD4 exome

AF:

0.344

AC:

AN:

Hom.:

Cov.:

AF XY:

0.280

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.667

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AF:

0.500

AC:

AN:

European-Finnish (FIN)

AF:

0.500

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.261

AC:

AN:

Other (OTH)

AF:

0.500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.555

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.306

AC:

46518

AN:

151778

Hom.:

7583

Cov.:

AF XY:

0.309

AC XY:

22950

AN XY:

74172

show subpopulations

African (AFR)

AF:

0.226

AC:

9353

AN:

41366

American (AMR)

AF:

0.359

AC:

5476

AN:

15262

Ashkenazi Jewish (ASJ)

AF:

0.347

AC:

1202

AN:

3468

East Asian (EAS)

AF:

0.474

AC:

2437

AN:

5146

South Asian (SAS)

AF:

0.256

AC:

1229

AN:

4800

European-Finnish (FIN)

AF:

0.365

AC:

3843

AN:

10538

Middle Eastern (MID)

AF:

0.228

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.324

AC:

21999

AN:

67900

Other (OTH)

AF:

0.304

AC:

638

AN:

2098

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1611

3222

4833

6444

8055

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

474

948

1422

1896

2370

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.325

Hom.:

15337

Bravo

AF:

0.311

Asia WGS

AF:

0.346

AC:

1199

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

3.8

(source)

DANN

Benign

0.53

PhyloP100

0.29

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over