Variant 7-150740839-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_018384.5(GIMAP5):c.-6-40C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.32 in 1,608,372 control chromosomes in the GnomAD database, including 85,861 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.38 ( 12080 hom., cov: 32)

Exomes 𝑓: 0.31 ( 73781 hom. )

Consequence

GIMAP5
NM_018384.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0650

Variant links:

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]

GIMAP5 links:

GIMAP1-GIMAP5 (HGNC:51257): (GIMAP1-GIMAP5 readthrough) This locus represents naturally occurring readthrough transcription between the neighboring GIMAP1 (GTPase, IMAP family member 1) and GIMAP5 (GTPase, IMAP family member 5) genes on chromosome 7. Alternative splicing results in multiple readthrough transcript variants, one of which encodes a fusion protein that shares sequence identity with each individual gene product. [provided by RefSeq, Jan 2015]

GIMAP1-GIMAP5 links:

GIMAP5 (HGNC:):

GIMAP5 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.548 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein	UniProt
GIMAP5	NM_018384.5 linkuse as main transcript	c.-6-40C>T	intron_variant	ENST00000358647.5	NP_060854.2	Q96F15-1A0A090N8P9
GIMAP1-GIMAP5	NM_001199577.2 linkuse as main transcript	c.607-40C>T	intron_variant		NP_001186506.1	A0A087WTJ2
GIMAP1-GIMAP5	NM_001303630.2 linkuse as main transcript	c.223-40C>T	intron_variant		NP_001290559.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GIMAP5	ENST00000358647.5 linkuse as main transcript	c.-6-40C>T		intron_variant		1	NM_018384.5	ENSP00000351473.3		Q96F15-1
GIMAP1-GIMAP5	ENST00000611999.4 linkuse as main transcript	c.607-40C>T		intron_variant		5		ENSP00000477920.1		A0A087WTJ2

Frequencies

GnomAD3 genomes

AF:

0.382

AC:

57936

AN:

151858

Hom.:

12059

Cov.:

show subpopulations

Gnomad AFR

AF:

0.554

Gnomad AMI

AF:

0.163

Gnomad AMR

AF:

0.286

Gnomad ASJ

AF:

0.344

Gnomad EAS

AF:

0.284

Gnomad SAS

AF:

0.395

Gnomad FIN

AF:

0.401

Gnomad MID

AF:

0.363

Gnomad NFE

AF:

0.308

Gnomad OTH

AF:

0.348

GnomAD3 exomes

AF:

0.327

AC:

82076

AN:

250770

Hom.:

14267

AF XY:

0.329

AC XY:

44603

AN XY:

135522

show subpopulations

Gnomad AFR exome

AF:

0.557

Gnomad AMR exome

AF:

0.228

Gnomad ASJ exome

AF:

0.321

Gnomad EAS exome

AF:

0.267

Gnomad SAS exome

AF:

0.377

Gnomad FIN exome

AF:

0.397

Gnomad NFE exome

AF:

0.309

Gnomad OTH exome

AF:

0.320

GnomAD4 exome

AF:

0.314

AC:

457015

AN:

1456396

Hom.:

73781

Cov.:

AF XY:

0.316

AC XY:

228980

AN XY:

724890

show subpopulations

Gnomad4 AFR exome

AF:

0.560

Gnomad4 AMR exome

AF:

0.236

Gnomad4 ASJ exome

AF:

0.325

Gnomad4 EAS exome

AF:

0.276

Gnomad4 SAS exome

AF:

0.376

Gnomad4 FIN exome

AF:

0.392

Gnomad4 NFE exome

AF:

0.302

Gnomad4 OTH exome

AF:

0.314

GnomAD4 genome

AF:

0.382

AC:

58010

AN:

151976

Hom.:

12080

Cov.:

AF XY:

0.385

AC XY:

28571

AN XY:

74276

show subpopulations

Gnomad4 AFR

AF:

0.554

Gnomad4 AMR

AF:

0.285

Gnomad4 ASJ

AF:

0.344

Gnomad4 EAS

AF:

0.285

Gnomad4 SAS

AF:

0.395

Gnomad4 FIN

AF:

0.401

Gnomad4 NFE

AF:

0.308

Gnomad4 OTH

AF:

0.350

Alfa

AF:

0.344

Hom.:

2047

Bravo

AF:

0.377

Asia WGS

AF:

0.357

AC:

1241

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.56

DANN

Benign

0.36

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over