rs6965571

chr7-150737384-G-A

Variant summary

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

The NM_001199577.2(GIMAP1-GIMAP5):c.403-121G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.156 in 715,118 control chromosomes in the GnomAD database, including 9,532 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 0.17 (2453 hom., cov: 31)
  • Exomes 𝑓: 0.15 (7079 hom.)
• Consequence: GIMAP1-GIMAP5 NM_001199577.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.74

Genes affected

GIMAP1-GIMAP5 (HGNC:):

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]

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 = 0.223 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GIMAP1-GIMAP5	NM_001199577.2	c.403-121G>A		intron_variant
GIMAP1-GIMAP5	NM_001303630.2	c.19-121G>A		intron_variant
GIMAP5	NM_018384.5			upstream_gene_variant		ENST00000358647.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GIMAP5	ENST00000498181.6	c.-210-121G>A		intron_variant		4		P1
GIMAP5	ENST00000358647.5			upstream_gene_variant		1	NM_018384.5	P1

Frequencies

GnomAD3 genomes AF: 0.174 AC: 26277 AN: 151388 Hom.: 2451 Cov.: 31

Gnomad AFR AF: 0.227

Gnomad AMI AF: 0.0735

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.0116

Gnomad SAS AF: 0.112

Gnomad FIN AF: 0.128

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.173

Gnomad OTH AF: 0.173

GnomAD4 exome AF: 0.151 AC: 85387 AN: 563670 Hom.: 7079 Cov.: 7 AF XY: 0.151 AC XY: 44520 AN XY: 295424

Gnomad4 AFR exome AF: 0.230

Gnomad4 AMR exome AF: 0.108

Gnomad4 ASJ exome AF: 0.181

Gnomad4 EAS exome AF: 0.00631

Gnomad4 SAS exome AF: 0.115

Gnomad4 FIN exome AF: 0.132

Gnomad4 NFE exome AF: 0.170

Gnomad4 OTH exome AF: 0.153

GnomAD4 genome AF: 0.174 AC: 26292 AN: 151448 Hom.: 2453 Cov.: 31 AF XY: 0.170 AC XY: 12532 AN XY: 73894

Gnomad4 AFR AF: 0.227

Gnomad4 AMR AF: 0.140

Gnomad4 ASJ AF: 0.188

Gnomad4 EAS AF: 0.0117

Gnomad4 SAS AF: 0.112

Gnomad4 FIN AF: 0.128

Gnomad4 NFE AF: 0.173

Gnomad4 OTH AF: 0.176

Alfa AF: 0.174 Hom.: 4711

Bravo AF: 0.175

Asia WGS AF: 0.0700 AC: 245 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	2.7
Dann	Benign	0.59

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: rs6965571; hg19: chr7-150434472;