NM_024711.6:c.710A>G

Variant names:

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_024711.6(GIMAP6):c.710A>G(p.Gln237Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00583 in 1,614,240 control chromosomes in the GnomAD database, including 506 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.031 ( 285 hom., cov: 33)

Exomes 𝑓: 0.0032 ( 221 hom. )

Consequence

GIMAP6
NM_024711.6 missense

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.427

Publications

8 publications found

Variant links:

Genes affected

GIMAP6 (HGNC:21918): (GTPase, IMAP family member 6) This gene encodes a member of the GTPases of immunity-associated proteins (GIMAP) family. GIMAP proteins contain GTP-binding and coiled-coil motifs, and may play roles in the regulation of cell survival. Decreased expression of this gene may play a role in non-small cell lung cancer. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene, which is found in a cluster with seven additional GIMAP genes on the long arm of chromosome 7. [provided by RefSeq, Sep 2011]

GIMAP6 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0017630458).

BP6

Variant 7-150627888-T-C is Benign according to our data. Variant chr7-150627888-T-C is described in ClinVar as [Benign]. Clinvar id is 776269.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.104 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GIMAP6	NM_024711.6 link	c.710A>G	p.Gln237Arg	missense_variant	Exon 3 of 3	ENST00000328902.9	NP_078987.3	Q6P9H5-1A0A090N7V4
GIMAP6	NM_001244072.2 link	c.920A>G	p.Gln307Arg	missense_variant	Exon 3 of 3		NP_001231001.1	Q6P9H5B4DH95
GIMAP6	NM_001244071.2 link	c.*297A>G		3_prime_UTR_variant	Exon 3 of 3		NP_001231000.1	Q6P9H5-3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
GIMAP6	ENST00000328902.9 link	c.710A>G	p.Gln237Arg	missense_variant	Exon 3 of 3	1	NM_024711.6	ENSP00000330374.5	Q6P9H5-1
GIMAP6	ENST00000618759.4 link	c.920A>G	p.Gln307Arg	missense_variant	Exon 3 of 3	2		ENSP00000479580.1	B4DH95
GIMAP6	ENST00000493969.2 link	c.*297A>G		3_prime_UTR_variant	Exon 3 of 3	2		ENSP00000418304.1	Q6P9H5-3

Frequencies

GnomAD3 genomes

AF:

0.0308

AC:

4687

AN:

152240

Hom.:

285

Cov.:

show subpopulations

Gnomad AFR

AF:

0.107

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0118

Gnomad ASJ

AF:

0.00115

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000207

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.0158

Gnomad NFE

AF:

0.000382

Gnomad OTH

AF:

0.0196

GnomAD2 exomes

AF:

0.00822

AC:

2066

AN:

251314

AF XY:

0.00604

show subpopulations

Gnomad AFR exome

AF:

0.108

Gnomad AMR exome

AF:

0.00651

Gnomad ASJ exome

AF:

0.000795

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000378

Gnomad OTH exome

AF:

0.00489

GnomAD4 exome

AF:

0.00323

AC:

4729

AN:

1461882

Hom.:

221

Cov.:

AF XY:

0.00282

AC XY:

2051

AN XY:

727246

show subpopulations

African (AFR)

AF:

0.111

AC:

3703

AN:

33480

American (AMR)

AF:

0.00637

AC:

285

AN:

44724

Ashkenazi Jewish (ASJ)

AF:

0.000459

AC:

AN:

26136

East Asian (EAS)

AF:

0.00

AC:

AN:

39700

South Asian (SAS)

AF:

0.000174

AC:

AN:

86258

European-Finnish (FIN)

AF:

0.00

AC:

AN:

53420

Middle Eastern (MID)

AF:

0.00693

AC:

AN:

5768

European-Non Finnish (NFE)

AF:

0.000225

AC:

250

AN:

1112000

Other (OTH)

AF:

0.00702

AC:

424

AN:

60396

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.485

Heterozygous variant carriers

285

570

856

1141

1426

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.0308

AC:

4689

AN:

152358

Hom.:

285

Cov.:

AF XY:

0.0296

AC XY:

2207

AN XY:

74508

show subpopulations

African (AFR)

AF:

0.107

AC:

4432

AN:

41582

American (AMR)

AF:

0.0118

AC:

180

AN:

15310

Ashkenazi Jewish (ASJ)

AF:

0.00115

AC:

AN:

3468

East Asian (EAS)

AF:

0.00

AC:

AN:

5186

South Asian (SAS)

AF:

0.000207

AC:

AN:

4826

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10632

Middle Eastern (MID)

AF:

0.0170

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.000382

AC:

AN:

68032

Other (OTH)

AF:

0.0194

AC:

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

217

434

652

869

1086

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.0110

Hom.:

266

Bravo

AF:

0.0358

TwinsUK

AF:

0.000539

AC:

ALSPAC

AF:

0.00

AC:

ESP6500AA

AF:

0.109

AC:

479

ESP6500EA

AF:

0.000465

AC:

ExAC

AF:

0.0100

AC:

1214

Asia WGS

AF:

0.00549

AC:

AN:

3478

EpiCase

AF:

0.000545

EpiControl

AF:

0.000711

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

Mar 02, 2018

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.072

BayesDel_addAF

Benign

-0.67

BayesDel_noAF

Benign

-0.65

CADD

Benign

0.14

(source)

DANN

Benign

0.21

DEOGEN2

Benign

0.00080

T;.

Eigen

Benign

-1.4

Eigen_PC

Benign

-1.4

FATHMM_MKL

Benign

0.052

LIST_S2

Benign

0.29

T;T

MetaRNN

Benign

0.0018

T;T

MetaSVM

Benign

-0.91

MutationAssessor

Benign

0.85

L;.

PhyloP100

-0.43

PrimateAI

Benign

0.21

PROVEAN

Benign

-1.0

N;.

REVEL

Benign

0.017

Sift

Benign

0.49

T;.

Sift4G

Benign

0.58

T;T

Polyphen

0.0020

B;.

Vest4

0.047

MVP

0.092

MPC

0.14

ClinPred

0.0013

GERP RS

-0.0074

Varity_R

0.062

gMVP

0.46

Mutation Taster

=100/0

polymorphism (auto)

(source)

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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NM_024711.6:c.710A>G

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over