rs9657891

chr7-150738385-A-Gchr7-150738385-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_018384.5(GIMAP5):c.-7+677A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.487 in 152,262 control chromosomes in the GnomAD database, including 18,810 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 0.49 (18785 hom., cov: 31)
  • Exomes 𝑓: 0.37 (25 hom.)
• Consequence: GIMAP5 NM_018384.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.644

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]

GIMAP1-GIMAP5 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.627 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GIMAP5	NM_018384.5	c.-7+677A>G		intron_variant		ENST00000358647.5
GIMAP1-GIMAP5	NM_001199577.2	c.606+677A>G		intron_variant
GIMAP1-GIMAP5	NM_001303630.2	c.222+677A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GIMAP5	ENST00000358647.5	c.-7+677A>G		intron_variant		1	NM_018384.5	P1

Frequencies

GnomAD3 genomes AF: 0.487 AC: 73895 AN: 151826 Hom.: 18764 Cov.: 31

Gnomad AFR AF: 0.633

Gnomad AMI AF: 0.281

Gnomad AMR AF: 0.416

Gnomad ASJ AF: 0.386

Gnomad EAS AF: 0.361

Gnomad SAS AF: 0.473

Gnomad FIN AF: 0.555

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.422

Gnomad OTH AF: 0.456

GnomAD4 exome AF: 0.371 AC: 118 AN: 318 Hom.: 25 Cov.: 0 AF XY: 0.351 AC XY: 47 AN XY: 134

Gnomad4 AMR exome AF: 0.367

Gnomad4 ASJ exome AF: 0.500

Gnomad4 SAS exome AF: 0.500

Gnomad4 FIN exome AF: 0.750

Gnomad4 NFE exome AF: 0.371

Gnomad4 OTH exome AF: 0.214

GnomAD4 genome AF: 0.487 AC: 73983 AN: 151944 Hom.: 18785 Cov.: 31 AF XY: 0.492 AC XY: 36538 AN XY: 74254

Gnomad4 AFR AF: 0.633

Gnomad4 AMR AF: 0.417

Gnomad4 ASJ AF: 0.386

Gnomad4 EAS AF: 0.362

Gnomad4 SAS AF: 0.473

Gnomad4 FIN AF: 0.555

Gnomad4 NFE AF: 0.422

Gnomad4 OTH AF: 0.456

Alfa AF: 0.455 Hom.: 3198

Bravo AF: 0.479

Asia WGS AF: 0.430 AC: 1495 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.87
Dann	Benign	0.57

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: rs9657891; hg19: chr7-150435473;