rs778778849

Variant names:

• chr7-150572366-C-A
• rs778778849
• NM_018326.3:c.296C>A

Your query was ambiguous. Multiple possible variants found:

• chr7-150572366-C-A
• chr7-150572366-C-G
• chr7-150572366-C-T

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_018326.3(GIMAP4):​c.296C>A​(p.Thr99Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 13/22 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T99M) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: GIMAP4 NM_018326.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.119

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]

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GIMAP4	NM_018326.3	c.296C>A	p.Thr99Lys	missense_variant	Exon 3 of 3	ENST00000255945.4	NP_060796.1
GIMAP4	NM_001363532.2	c.338C>A	p.Thr113Lys	missense_variant	Exon 3 of 3		NP_001350461.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GIMAP4	ENST00000255945.4	c.296C>A	p.Thr99Lys	missense_variant	Exon 3 of 3	1	NM_018326.3	ENSP00000255945.2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.43
BayesDel_addAF	Benign	-0.0065	T
BayesDel_noAF	Benign	-0.25
CADD	Benign	18
DANN	Benign	0.96
DEOGEN2	Benign	0.17	T;.;.
Eigen	Benign	-0.31
Eigen_PC	Benign	-0.51
FATHMM_MKL	Benign	0.059	N
LIST_S2	Benign	0.52	T;T;T
M_CAP	Benign	0.066	D
MetaRNN	Uncertain	0.43	T;T;T
MetaSVM	Benign	-0.79	T
MutationAssessor	Uncertain	2.3	M;.;.
PhyloP100		0.12
PrimateAI	Benign	0.35	T
PROVEAN	Pathogenic	-4.7	D;D;D
REVEL	Benign	0.26
Sift	Uncertain	0.0020	D;D;T
Sift4G	Uncertain	0.0080	D;D;T
Polyphen		1.0	D;D;.
Vest4		0.41
MutPred		0.57		.;Gain of ubiquitination at T113 (P = 0.0121);Gain of ubiquitination at T113 (P = 0.0121);
MVP		0.77
MPC		0.36
ClinPred		0.98	D
GERP RS		3.7
Varity_R		0.82
gMVP		0.72
Mutation Taster		=92/8	polymorphism

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

Publications

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Other links and lift over

dbSNP: rs778778849; hg19: chr7-150269454;