rs9657886

chr7-150741470-G-T

Variant summary

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

The NM_018384.5(GIMAP5):c.43+543G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.313 in 152,004 control chromosomes in the GnomAD database, including 7,661 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 0.31 (7661 hom., cov: 32)
• Consequence: GIMAP5 NM_018384.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.30

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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.333 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GIMAP5	NM_018384.5	c.43+543G>T		intron_variant		ENST00000358647.5
GIMAP1-GIMAP5	NM_001199577.2	c.655+543G>T		intron_variant
GIMAP1-GIMAP5	NM_001303630.2	c.271+543G>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GIMAP5	ENST00000358647.5	c.43+543G>T		intron_variant		1	NM_018384.5	P1

Frequencies

GnomAD3 genomes AF: 0.313 AC: 47579 AN: 151886 Hom.: 7655 Cov.: 32

Gnomad AFR AF: 0.337

Gnomad AMI AF: 0.164

Gnomad AMR AF: 0.261

Gnomad ASJ AF: 0.332

Gnomad EAS AF: 0.272

Gnomad SAS AF: 0.242

Gnomad FIN AF: 0.401

Gnomad MID AF: 0.318

Gnomad NFE AF: 0.306

Gnomad OTH AF: 0.301

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.313 AC: 47627 AN: 152004 Hom.: 7661 Cov.: 32 AF XY: 0.316 AC XY: 23496 AN XY: 74280

Gnomad4 AFR AF: 0.337

Gnomad4 AMR AF: 0.260

Gnomad4 ASJ AF: 0.332

Gnomad4 EAS AF: 0.273

Gnomad4 SAS AF: 0.243

Gnomad4 FIN AF: 0.401

Gnomad4 NFE AF: 0.306

Gnomad4 OTH AF: 0.303

Alfa AF: 0.304 Hom.: 7031

Bravo AF: 0.303

Asia WGS AF: 0.258 AC: 898 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	0.56
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: rs9657886; hg19: chr7-150438558;