Variant chr7-150520221-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_153236.4(GIMAP7):c.247C>T(p.Arg83Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.227 in 1,613,840 control chromosomes in the GnomAD database, including 43,711 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.19 ( 3501 hom., cov: 32)

Exomes 𝑓: 0.23 ( 40210 hom. )

Consequence

GIMAP7
NM_153236.4 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -1.09

Variant links:

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]

GIMAP7 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.015388012).

BP6

Variant 7-150520221-C-T is Benign according to our data. Variant chr7-150520221-C-T is described in ClinVar as [Benign]. Clinvar id is 1294549.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.261 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GIMAP7	NM_153236.4 linkuse as main transcript	c.247C>T	p.Arg83Cys	missense_variant	2/2	ENST00000313543.5	NP_694968.1	Q8NHV1A0A090N8P8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GIMAP7	ENST00000313543.5 linkuse as main transcript	c.247C>T	p.Arg83Cys	missense_variant	2/2	1	NM_153236.4	ENSP00000315474.4		Q8NHV1

Frequencies

GnomAD3 genomes

AF:

0.190

AC:

28834

AN:

152004

Hom.:

3504

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0445

Gnomad AMI

AF:

0.284

Gnomad AMR

AF:

0.268

Gnomad ASJ

AF:

0.267

Gnomad EAS

AF:

0.151

Gnomad SAS

AF:

0.233

Gnomad FIN

AF:

0.339

Gnomad MID

AF:

0.184

Gnomad NFE

AF:

0.233

Gnomad OTH

AF:

0.168

GnomAD3 exomes

AF:

0.235

AC:

58956

AN:

251096

Hom.:

7582

AF XY:

0.236

AC XY:

32062

AN XY:

135716

show subpopulations

Gnomad AFR exome

AF:

0.0395

Gnomad AMR exome

AF:

0.315

Gnomad ASJ exome

AF:

0.256

Gnomad EAS exome

AF:

0.153

Gnomad SAS exome

AF:

0.240

Gnomad FIN exome

AF:

0.333

Gnomad NFE exome

AF:

0.230

Gnomad OTH exome

AF:

0.235

GnomAD4 exome

AF:

0.231

AC:

337032

AN:

1461718

Hom.:

40210

Cov.:

AF XY:

0.231

AC XY:

167883

AN XY:

727150

show subpopulations

Gnomad4 AFR exome

AF:

0.0374

Gnomad4 AMR exome

AF:

0.311

Gnomad4 ASJ exome

AF:

0.257

Gnomad4 EAS exome

AF:

0.164

Gnomad4 SAS exome

AF:

0.240

Gnomad4 FIN exome

AF:

0.329

Gnomad4 NFE exome

AF:

0.230

Gnomad4 OTH exome

AF:

0.226

GnomAD4 genome

AF:

0.190

AC:

28831

AN:

152122

Hom.:

3501

Cov.:

AF XY:

0.196

AC XY:

14548

AN XY:

74358

show subpopulations

Gnomad4 AFR

AF:

0.0445

Gnomad4 AMR

AF:

0.267

Gnomad4 ASJ

AF:

0.267

Gnomad4 EAS

AF:

0.151

Gnomad4 SAS

AF:

0.232

Gnomad4 FIN

AF:

0.339

Gnomad4 NFE

AF:

0.233

Gnomad4 OTH

AF:

0.167

Alfa

AF:

0.215

Hom.:

9291

Bravo

AF:

0.179

TwinsUK

AF:

0.224

AC:

831

ALSPAC

AF:

0.217

AC:

836

ESP6500AA

AF:

0.0495

AC:

218

ESP6500EA

AF:

0.228

AC:

1961

ExAC

AF:

0.226

AC:

27395

Asia WGS

AF:

0.172

AC:

599

AN:

3478

EpiCase

AF:

0.222

EpiControl

AF:

0.221

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Feb 18, 2020	This variant is associated with the following publications: (PMID: 31178129) -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.19

BayesDel_addAF

Benign

-0.71

BayesDel_noAF

Benign

-0.64

CADD

Benign

DANN

Uncertain

0.98

DEOGEN2

Benign

0.063

Eigen

Benign

-0.85

Eigen_PC

Benign

-1.2

FATHMM_MKL

Benign

0.027

LIST_S2

Uncertain

0.87

MetaRNN

Benign

0.015

MetaSVM

Benign

-0.98

MutationAssessor

Pathogenic

3.7

PrimateAI

Benign

0.24

PROVEAN

Pathogenic

-6.2

REVEL

Benign

0.14

Sift

Pathogenic

0.0

Sift4G

Pathogenic

0.0010

Polyphen

1.0

Vest4

0.093

MPC

0.83

ClinPred

0.14

GERP RS

-10

Varity_R

0.43

gMVP

0.20

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over