chr7-150743155-G-C

Position:

• chr7-150743155-G-C

Variant summary

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

The NM_018384.5(GIMAP5):​c.*92G>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.311 in 1,469,250 control chromosomes in the GnomAD database, including 73,330 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 0.37 (11390 hom., cov: 31)
  • Exomes 𝑓: 0.30 (61940 hom.)
• Consequence: GIMAP5 NM_018384.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.57

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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.53 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GIMAP5	NM_018384.5	c.*92G>C		3_prime_UTR_variant	3/3	ENST00000358647.5
GIMAP1-GIMAP5	NM_001199577.2	c.*92G>C		3_prime_UTR_variant	6/6
GIMAP1-GIMAP5	NM_001303630.2	c.*92G>C		3_prime_UTR_variant	5/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GIMAP5	ENST00000358647.5	c.*92G>C		3_prime_UTR_variant	3/3	1	NM_018384.5	P1

Frequencies

GnomAD3 genomes AF: 0.371 AC: 56240 AN: 151782 Hom.: 11372 Cov.: 31

Gnomad AFR AF: 0.536

Gnomad AMI AF: 0.163

Gnomad AMR AF: 0.281

Gnomad ASJ AF: 0.345

Gnomad EAS AF: 0.283

Gnomad SAS AF: 0.265

Gnomad FIN AF: 0.401

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.305

Gnomad OTH AF: 0.340

GnomAD4 exome AF: 0.304 AC: 400519 AN: 1317350 Hom.: 61940 Cov.: 21 AF XY: 0.303 AC XY: 196260 AN XY: 648170

Gnomad4 AFR exome AF: 0.545

Gnomad4 AMR exome AF: 0.236

Gnomad4 ASJ exome AF: 0.327

Gnomad4 EAS exome AF: 0.275

Gnomad4 SAS exome AF: 0.259

Gnomad4 FIN exome AF: 0.390

Gnomad4 NFE exome AF: 0.300

Gnomad4 OTH exome AF: 0.304

GnomAD4 genome AF: 0.371 AC: 56313 AN: 151900 Hom.: 11390 Cov.: 31 AF XY: 0.372 AC XY: 27583 AN XY: 74218

Gnomad4 AFR AF: 0.536

Gnomad4 AMR AF: 0.280

Gnomad4 ASJ AF: 0.345

Gnomad4 EAS AF: 0.284

Gnomad4 SAS AF: 0.266

Gnomad4 FIN AF: 0.401

Gnomad4 NFE AF: 0.305

Gnomad4 OTH AF: 0.342

Alfa AF: 0.197 Hom.: 434

Bravo AF: 0.370

Asia WGS AF: 0.294 AC: 1024 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.16
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: rs10361; hg19: chr7-150440243; COSMIC: COSV57529642; COSMIC: COSV57529642;