7-150742584-C-G

Position:

• chr7-150742584-C-G

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4 BP6

The NM_018384.5(GIMAP5):​c.445C>G​(p.Leu149Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).

• Frequency: Genomes: not found (cov: 32)
• Consequence: GIMAP5 NM_018384.5 missense
• Clinical Significance: Likely benign no assertion criteria provided B:1
• Conservation: PhyloP100: 0.0880

Genes affected

GIMAP5 (HGNC:18005): (GTPase, IMAP family member 5) This gene encodes a protein belonging to the GTP-binding superfamily and to the immuno-associated nucleotide (IAN) subfamily of nucleotide-binding proteins. In humans, the IAN subfamily genes are located in a cluster at 7q36.1. This gene encodes an antiapoptotic protein that functions in T-cell survival. Polymorphisms in this gene are associated with systemic lupus erythematosus. Read-through transcription exists between this gene and the neighboring upstream GIMAP1 (GTPase, IMAP family member 1) gene. [provided by RefSeq, Dec 2010]

GIMAP1-GIMAP5 (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.36672154).
• BP6: Variant 7-150742584-C-G is Benign according to our data. Variant chr7-150742584-C-G is described in ClinVar as [Likely_benign]. Clinvar id is 2681295.Status of the report is no_assertion_criteria_provided, 0 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GIMAP5	NM_018384.5	c.445C>G	p.Leu149Val	missense_variant	3/3	ENST00000358647.5
GIMAP1-GIMAP5	NM_001199577.2	c.1057C>G	p.Leu353Val	missense_variant	6/6
GIMAP1-GIMAP5	NM_001303630.2	c.673C>G	p.Leu225Val	missense_variant	5/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GIMAP5	ENST00000358647.5	c.445C>G	p.Leu149Val	missense_variant	3/3	1	NM_018384.5	P1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 75

GnomAD4 genome Cov.: 32

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

Submissions by phenotype

EBV-positive nodal T- and NK-cell lymphoma Benign:1

Likely benign, no assertion criteria provided

research

Department of Clinical Pathology, School of Medicine, Fujita Health University

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.12
BayesDel_addAF	Benign	-0.13	T
BayesDel_noAF	Benign	-0.42
CADD	Benign	16
DANN	Uncertain	1.0
DEOGEN2	Benign	0.097	.;T;T
Eigen	Benign	0.018
Eigen_PC	Benign	-0.079
FATHMM_MKL	Benign	0.24	N
LIST_S2	Benign	0.67	T;.;T
M_CAP	Benign	0.0025	T
MetaRNN	Benign	0.37	T;T;T
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	2.0	.;M;M
MutationTaster	Benign	0.85	N
PrimateAI	Benign	0.44	T
PROVEAN	Benign	-1.6	.;.;N
REVEL	Benign	0.16
Sift	Benign	0.21	.;.;T
Sift4G	Benign	0.15	T;T;T
Polyphen		1.0	.;D;D
Vest4		0.56
MutPred		0.60		.;Loss of stability (P = 0.0648);Loss of stability (P = 0.0648);
MVP		0.17
MPC		0.16
ClinPred		0.73	D
GERP RS		3.3
Varity_R		0.19
gMVP		0.22

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr7-150439672;