Genetic Variant GIMAP4:c.58+183T>A (chr7-150570142-T-A) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_018326.3(GIMAP4):c.58+183T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000433 in 462,088 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 31)

Exomes 𝑓: 0.0000043 ( 0 hom. )

Consequence

GIMAP4
NM_018326.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.02

Publications

1 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: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GIMAP4	NM_018326.3 link	c.58+183T>A		intron_variant	Intron 2 of 2	ENST00000255945.4	NP_060796.1	Q9NUV9A0A090N7X0
GIMAP4	NM_001363532.2 link	c.100+141T>A		intron_variant	Intron 2 of 2		NP_001350461.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GIMAP4	ENST00000255945.4 link	c.58+183T>A		intron_variant	Intron 2 of 2	1	NM_018326.3	ENSP00000255945.2		Q9NUV9

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

0.00000433

AC:

AN:

462088

Hom.:

AF XY:

0.00000814

AC XY:

AN XY:

245736

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

13044

American (AMR)

AF:

0.00

AC:

AN:

22660

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

14366

East Asian (EAS)

AF:

0.00

AC:

AN:

31026

South Asian (SAS)

AF:

0.0000210

AC:

AN:

47708

European-Finnish (FIN)

AF:

0.00

AC:

AN:

29864

Middle Eastern (MID)

AF:

0.00

AC:

AN:

1968

European-Non Finnish (NFE)

AF:

0.00000364

AC:

AN:

274904

Other (OTH)

AF:

0.00

AC:

AN:

26548

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.625

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

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

Cov.:

Alfa

AF:

0.00

Hom.:

110

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

5.4

(source)

DANN

Benign

0.69

PhyloP100

1.0

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over