7-150628087-C-T

Variant names:

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_024711.6(GIMAP6):c.511G>A(p.Gly171Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.207 in 1,614,018 control chromosomes in the GnomAD database, including 36,116 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in UniProt.

Frequency

Genomes: 𝑓 0.18 ( 2995 hom., cov: 33)

Exomes 𝑓: 0.21 ( 33121 hom. )

Consequence

GIMAP6
NM_024711.6 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.144

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 made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0073738396).

BP6

Variant 7-150628087-C-T is Benign according to our data. Variant chr7-150628087-C-T is described in ClinVar as [Benign]. Clinvar id is 2688132.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.245 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GIMAP6	NM_024711.6 link	c.511G>A	p.Gly171Ser	missense_variant	Exon 3 of 3	ENST00000328902.9	NP_078987.3	Q6P9H5-1A0A090N7V4
GIMAP6	NM_001244072.2 link	c.721G>A	p.Gly241Ser	missense_variant	Exon 3 of 3		NP_001231001.1	Q6P9H5B4DH95
GIMAP6	NM_001244071.2 link	c.*98G>A		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.511G>A	p.Gly171Ser	missense_variant	Exon 3 of 3	1	NM_024711.6	ENSP00000330374.5	Q6P9H5-1
GIMAP6	ENST00000618759.4 link	c.721G>A	p.Gly241Ser	missense_variant	Exon 3 of 3	2		ENSP00000479580.1	B4DH95
GIMAP6	ENST00000493969 link	c.*98G>A		3_prime_UTR_variant	Exon 3 of 3	2		ENSP00000418304.1	Q6P9H5-3

Frequencies

GnomAD3 genomes

AF:

0.183

AC:

27864

AN:

152054

Hom.:

2998

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0807

Gnomad AMI

AF:

0.232

Gnomad AMR

AF:

0.251

Gnomad ASJ

AF:

0.202

Gnomad EAS

AF:

0.175

Gnomad SAS

AF:

0.218

Gnomad FIN

AF:

0.315

Gnomad MID

AF:

0.152

Gnomad NFE

AF:

0.207

Gnomad OTH

AF:

0.157

GnomAD3 exomes

AF:

0.221

AC:

55397

AN:

251068

Hom.:

6655

AF XY:

0.221

AC XY:

29929

AN XY:

135682

show subpopulations

Gnomad AFR exome

AF:

0.0767

Gnomad AMR exome

AF:

0.299

Gnomad ASJ exome

AF:

0.200

Gnomad EAS exome

AF:

0.179

Gnomad SAS exome

AF:

0.228

Gnomad FIN exome

AF:

0.314

Gnomad NFE exome

AF:

0.207

Gnomad OTH exome

AF:

0.210

GnomAD4 exome

AF:

0.209

AC:

305913

AN:

1461846

Hom.:

33121

Cov.:

AF XY:

0.209

AC XY:

152160

AN XY:

727218

show subpopulations

Gnomad4 AFR exome

AF:

0.0753

Gnomad4 AMR exome

AF:

0.297

Gnomad4 ASJ exome

AF:

0.200

Gnomad4 EAS exome

AF:

0.182

Gnomad4 SAS exome

AF:

0.228

Gnomad4 FIN exome

AF:

0.309

Gnomad4 NFE exome

AF:

0.205

Gnomad4 OTH exome

AF:

0.206

GnomAD4 genome

AF:

0.183

AC:

27864

AN:

152172

Hom.:

2995

Cov.:

AF XY:

0.189

AC XY:

14091

AN XY:

74386

show subpopulations

Gnomad4 AFR

AF:

0.0806

Gnomad4 AMR

AF:

0.251

Gnomad4 ASJ

AF:

0.202

Gnomad4 EAS

AF:

0.175

Gnomad4 SAS

AF:

0.218

Gnomad4 FIN

AF:

0.315

Gnomad4 NFE

AF:

0.207

Gnomad4 OTH

AF:

0.157

Alfa

AF:

0.197

Hom.:

4622

Bravo

AF:

0.175

TwinsUK

AF:

0.201

AC:

745

ALSPAC

AF:

0.197

AC:

760

ESP6500AA

AF:

0.0867

AC:

382

ESP6500EA

AF:

0.204

AC:

1755

ExAC

AF:

0.213

AC:

25900

Asia WGS

AF:

0.201

AC:

701

AN:

3478

EpiCase

AF:

0.192

EpiControl

AF:

0.191

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Benign:1

Jan 24, 2024

Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is classified as Benign based on local population frequency. This variant was detected in 48% of patients studied by a panel of primary immunodeficiencies. Number of patients: 46. Only high quality variants are reported. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.14

BayesDel_addAF

Benign

-0.80

BayesDel_noAF

Benign

-0.77

CADD

Benign

DANN

Uncertain

0.99

DEOGEN2

Benign

0.0054

T;.

Eigen

Benign

-0.55

Eigen_PC

Benign

-0.67

FATHMM_MKL

Benign

0.13

LIST_S2

Benign

0.54

T;T

MetaRNN

Benign

0.0074

T;T

MetaSVM

Benign

-0.95

MutationAssessor

Benign

1.8

L;.

PrimateAI

Benign

0.40

PROVEAN

Uncertain

-3.1

D;.

REVEL

Benign

0.082

Sift

Benign

0.075

T;.

Sift4G

Uncertain

0.048

D;T

Polyphen

0.70

P;.

Vest4

0.14

MPC

0.58

ClinPred

0.030

GERP RS

3.4

Varity_R

0.19

gMVP

0.49

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