Genetic Variant GIMAP4:c.59-57G>T (chr7-150572072-G-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_018326.3(GIMAP4):c.59-57G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.226 in 1,129,688 control chromosomes in the GnomAD database, including 29,644 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 0.25 ( 4863 hom., cov: 32)

Exomes 𝑓: 0.22 ( 24781 hom. )

Consequence

GIMAP4
NM_018326.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.23

Publications

5 publications found

Variant links:

Genes affected

GIMAP4 (HGNC:21872): (GTPase, IMAP family member 4) This gene encodes a protein belonging to the GTP-binding superfamily and to the immuno-associated nucleotide (IAN) subfamily of nucleotide-binding proteins. The encoded protein of this gene may be negatively regulated by T-cell acute lymphocytic leukemia 1 (TAL1). In humans, the IAN subfamily genes are located in a cluster at 7q36.1. [provided by RefSeq, Jul 2008]

GIMAP4 links:

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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=-0.89).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.304 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018326.3. 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
	GIMAP4	NM_018326.3	MANE Select	c.59-57G>T		intron	N/A	NP_060796.1	Q9NUV9
	GIMAP4	NM_001363532.2		c.101-57G>T		intron	N/A	NP_001350461.1	G5E9W9

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
GIMAP4	ENST00000255945.4	TSL:1 MANE Select	c.59-57G>T	intron	N/A	ENSP00000255945.2	Q9NUV9
GIMAP4	ENST00000461940.5	TSL:2	c.101-57G>T	intron	N/A	ENSP00000419545.1	G5E9W9
GIMAP4	ENST00000851189.1		c.59-57G>T	intron	N/A	ENSP00000521248.1

Frequencies

GnomAD3 genomes

AF:

0.248

AC:

37710

AN:

151804

Hom.:

4852

Cov.:

show subpopulations

Gnomad AFR

AF:

0.309

Gnomad AMI

AF:

0.207

Gnomad AMR

AF:

0.227

Gnomad ASJ

AF:

0.225

Gnomad EAS

AF:

0.297

Gnomad SAS

AF:

0.229

Gnomad FIN

AF:

0.238

Gnomad MID

AF:

0.244

Gnomad NFE

AF:

0.218

Gnomad OTH

AF:

0.227

GnomAD4 exome

AF:

0.223

AC:

217580

AN:

977768

Hom.:

24781

AF XY:

0.223

AC XY:

111229

AN XY:

499568

show subpopulations

African (AFR)

AF:

0.307

AC:

7081

AN:

23064

American (AMR)

AF:

0.207

AC:

7025

AN:

33858

Ashkenazi Jewish (ASJ)

AF:

0.224

AC:

4270

AN:

19058

East Asian (EAS)

AF:

0.310

AC:

11612

AN:

37426

South Asian (SAS)

AF:

0.223

AC:

14372

AN:

64508

European-Finnish (FIN)

AF:

0.228

AC:

10065

AN:

44148

Middle Eastern (MID)

AF:

0.226

AC:

1062

AN:

4690

European-Non Finnish (NFE)

AF:

0.216

AC:

152432

AN:

707156

Other (OTH)

AF:

0.220

AC:

9661

AN:

43860

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

9093

18186

27278

36371

45464

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

4472

8944

13416

17888

22360

<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:

0.249

AC:

37758

AN:

151920

Hom.:

4863

Cov.:

AF XY:

0.250

AC XY:

18524

AN XY:

74232

show subpopulations

African (AFR)

AF:

0.309

AC:

12785

AN:

41402

American (AMR)

AF:

0.227

AC:

3472

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.225

AC:

782

AN:

3468

East Asian (EAS)

AF:

0.298

AC:

1536

AN:

5158

South Asian (SAS)

AF:

0.230

AC:

1107

AN:

4822

European-Finnish (FIN)

AF:

0.238

AC:

2515

AN:

10546

Middle Eastern (MID)

AF:

0.231

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.218

AC:

14815

AN:

67928

Other (OTH)

AF:

0.232

AC:

489

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1408

2816

4223

5631

7039

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

388

776

1164

1552

1940

<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:

0.235

Hom.:

687

Bravo

AF:

0.251

Asia WGS

AF:

0.250

AC:

868

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.44

(source)

DANN

Benign

0.63

PhyloP100

-1.2

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