7-150728263-G-T

Position:

• chr7-150728263-G-T

Variant summary

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

The NM_001199577.2(GIMAP1-GIMAP5):​c.402+7857G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.108 in 152,246 control chromosomes in the GnomAD database, including 994 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 (994 hom., cov: 32)
• Consequence: GIMAP1-GIMAP5 NM_001199577.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.507

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=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.188 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GIMAP1-GIMAP5	NM_001199577.2	c.402+7857G>T		intron_variant
GIMAP1-GIMAP5	NM_001303630.2	c.18+9173G>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GIMAP5	ENST00000498181.6	c.-211+5893G>T		intron_variant		4		P1

Frequencies

GnomAD3 genomes AF: 0.108 AC: 16431 AN: 152128 Hom.: 994 Cov.: 32

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.0802

Gnomad AMR AF: 0.0958

Gnomad ASJ AF: 0.0876

Gnomad EAS AF: 0.197

Gnomad SAS AF: 0.100

Gnomad FIN AF: 0.108

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0945

Gnomad OTH AF: 0.114

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

GnomAD4 genome AF: 0.108 AC: 16460 AN: 152246 Hom.: 994 Cov.: 32 AF XY: 0.109 AC XY: 8112 AN XY: 74440

Gnomad4 AFR AF: 0.127

Gnomad4 AMR AF: 0.0956

Gnomad4 ASJ AF: 0.0876

Gnomad4 EAS AF: 0.198

Gnomad4 SAS AF: 0.101

Gnomad4 FIN AF: 0.108

Gnomad4 NFE AF: 0.0945

Gnomad4 OTH AF: 0.115

Alfa AF: 0.0953 Hom.: 769

Bravo AF: 0.109

Asia WGS AF: 0.156 AC: 543 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	2.4
DANN	Benign	0.79

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: rs6945478; hg19: chr7-150425351;