rs6598

chr7-150743561-G-Achr7-150743561-G-Cchr7-150743561-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.*498G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.38 in 153,836 control chromosomes in the GnomAD database, including 12,134 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 (12086 hom., cov: 32)
  • Exomes 𝑓: 0.23 (48 hom.)
• Consequence: GIMAP5 NM_018384.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.96

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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.547 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GIMAP5	NM_018384.5	c.*498G>A		3_prime_UTR_variant	3/3	ENST00000358647.5
GIMAP1-GIMAP5	NM_001199577.2	c.*498G>A		3_prime_UTR_variant	6/6
GIMAP1-GIMAP5	NM_001303630.2	c.*498G>A		3_prime_UTR_variant	5/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GIMAP5	ENST00000358647.5	c.*498G>A		3_prime_UTR_variant	3/3	1	NM_018384.5	P1

Frequencies

GnomAD3 genomes AF: 0.381 AC: 57960 AN: 151958 Hom.: 12065 Cov.: 32

Gnomad AFR AF: 0.553

Gnomad AMI AF: 0.164

Gnomad AMR AF: 0.286

Gnomad ASJ AF: 0.345

Gnomad EAS AF: 0.284

Gnomad SAS AF: 0.395

Gnomad FIN AF: 0.401

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.308

Gnomad OTH AF: 0.348

GnomAD4 exome AF: 0.230 AC: 404 AN: 1760 Hom.: 48 Cov.: 0 AF XY: 0.222 AC XY: 195 AN XY: 878

Gnomad4 AFR exome AF: 0.357

Gnomad4 AMR exome AF: 0.138

Gnomad4 ASJ exome AF: 0.375

Gnomad4 EAS exome AF: 0.0714

Gnomad4 SAS exome AF: 0.256

Gnomad4 FIN exome AF: 0.400

Gnomad4 NFE exome AF: 0.243

Gnomad4 OTH exome AF: 0.226

GnomAD4 genome AF: 0.382 AC: 58034 AN: 152076 Hom.: 12086 Cov.: 32 AF XY: 0.384 AC XY: 28566 AN XY: 74306

Gnomad4 AFR AF: 0.553

Gnomad4 AMR AF: 0.285

Gnomad4 ASJ AF: 0.345

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: 0.273 Hom.: 1418

Bravo AF: 0.377

Asia WGS AF: 0.356 AC: 1239 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.32
Dann	Benign	0.48

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: rs6598; hg19: chr7-150440649;