rs769439572

Variant names:

• chr7-150520141-G-A
• rs769439572
• NM_153236.4:c.167G>A

Your query was ambiguous. Multiple possible variants found:

• chr7-150520141-G-A
• chr7-150520141-G-C

Variant summary

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

The NM_153236.4(GIMAP7):​c.167G>A​(p.Gly56Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 14/21 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. G56A) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: GIMAP7 NM_153236.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.54

Genes affected

GIMAP7 (HGNC:22404): (GTPase, IMAP family member 7) 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. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Uncertain_significance. Variant got 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
GIMAP7	NM_153236.4	c.167G>A	p.Gly56Glu	missense_variant	Exon 2 of 2	ENST00000313543.5	NP_694968.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GIMAP7	ENST00000313543.5	c.167G>A	p.Gly56Glu	missense_variant	Exon 2 of 2	1	NM_153236.4	ENSP00000315474.4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.30
BayesDel_addAF	Benign	-0.11	T
BayesDel_noAF	Benign	-0.40
CADD	Benign	15
DANN	Benign	0.90
DEOGEN2	Benign	0.070	T
Eigen	Benign	-0.099
Eigen_PC	Benign	-0.21
FATHMM_MKL	Benign	0.63	D
LIST_S2	Benign	0.65	T
M_CAP	Benign	0.045	D
MetaRNN	Uncertain	0.43	T
MetaSVM	Benign	-0.79	T
MutationAssessor	Benign	2.0	M
PrimateAI	Benign	0.41	T
PROVEAN	Uncertain	-4.3	D
REVEL	Benign	0.23
Sift	Benign	0.42	T
Sift4G	Benign	0.27	T
Polyphen		0.98	D
Vest4		0.19
MutPred		0.73		Gain of solvent accessibility (P = 0.0456);
MVP		0.79
MPC		0.57
ClinPred		0.43	T
GERP RS		3.3
Varity_R		0.23
gMVP		0.31

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

LitVar

Other links and lift over

dbSNP: rs769439572; hg19: chr7-150217229; COSMIC: COSV100543752;