rs2286900

Positions:

• chr7-150720957-G-A

Variant summary

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

The NM_130759.4(GIMAP1):​c.*32G>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 0.0998 in 1,475,006 control chromosomes in the GnomAD database, including 7,735 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 0.11 (1010 hom., cov: 32)
  • Exomes 𝑓: 0.099 (6725 hom.)
• Consequence: GIMAP1 NM_130759.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.01

Genes affected

GIMAP1 (HGNC:23237): (GTPase, IMAP family member 1) 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 is thought to be involved in the differentiation of T helper (Th) cells of the Th1 lineage, and the related mouse gene has been shown to be critical for the development of mature B and T lymphocytes. Read-through transcription exists between this gene and the downstream GIMAP5 (GTPase, IMAP family member 5) 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 (EAS) allele frequency at 95% confidence interval = 0.187 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GIMAP1	NM_130759.4	c.*32G>A		3_prime_UTR_variant	3/3	ENST00000307194.6
GIMAP1-GIMAP5	NM_001199577.2	c.402+551G>A		intron_variant
GIMAP1-GIMAP5	NM_001303630.2	c.18+1867G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GIMAP1	ENST00000307194.6	c.*32G>A		3_prime_UTR_variant	3/3	1	NM_130759.4	P1

Frequencies

GnomAD3 genomes AF: 0.109 AC: 16524 AN: 152094 Hom.: 1010 Cov.: 32

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.0822

Gnomad AMR AF: 0.0974

Gnomad ASJ AF: 0.0879

Gnomad EAS AF: 0.197

Gnomad SAS AF: 0.100

Gnomad FIN AF: 0.108

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0955

Gnomad OTH AF: 0.114

GnomAD3 exomes AF: 0.109 AC: 14504 AN: 133184 Hom.: 794 AF XY: 0.106 AC XY: 7787 AN XY: 73538

Gnomad AFR exome AF: 0.123

Gnomad AMR exome AF: 0.102

Gnomad ASJ exome AF: 0.0771

Gnomad EAS exome AF: 0.197

Gnomad SAS exome AF: 0.100

Gnomad FIN exome AF: 0.108

Gnomad NFE exome AF: 0.0960

Gnomad OTH exome AF: 0.107

GnomAD4 exome AF: 0.0988 AC: 130675 AN: 1322794 Hom.: 6725 Cov.: 28 AF XY: 0.0987 AC XY: 63901 AN XY: 647636

Gnomad4 AFR exome AF: 0.125

Gnomad4 AMR exome AF: 0.100

Gnomad4 ASJ exome AF: 0.0831

Gnomad4 EAS exome AF: 0.191

Gnomad4 SAS exome AF: 0.0986

Gnomad4 FIN exome AF: 0.108

Gnomad4 NFE exome AF: 0.0949

Gnomad4 OTH exome AF: 0.0992

GnomAD4 genome AF: 0.109 AC: 16552 AN: 152212 Hom.: 1010 Cov.: 32 AF XY: 0.109 AC XY: 8149 AN XY: 74438

Gnomad4 AFR AF: 0.127

Gnomad4 AMR AF: 0.0972

Gnomad4 ASJ AF: 0.0879

Gnomad4 EAS AF: 0.197

Gnomad4 SAS AF: 0.101

Gnomad4 FIN AF: 0.108

Gnomad4 NFE AF: 0.0955

Gnomad4 OTH AF: 0.115

Alfa AF: 0.0945 Hom.: 749

Bravo AF: 0.109

Asia WGS AF: 0.156 AC: 545 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	3.8
DANN	Benign	0.65

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: rs2286900; hg19: chr7-150418045;