rs9657891

Positions:

• chr7-150738385-A-G
• chr7-150738385-A-T

Variant summary

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

The NM_018384.5(GIMAP5):​c.-7+677A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.487 in 152,262 control chromosomes in the GnomAD database, including 18,810 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 0.49 (18785 hom., cov: 31)
  • Exomes 𝑓: 0.37 (25 hom.)
• Consequence: GIMAP5 NM_018384.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.644

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:51257): (GIMAP1-GIMAP5 readthrough) This locus represents naturally occurring readthrough transcription between the neighboring GIMAP1 (GTPase, IMAP family member 1) and GIMAP5 (GTPase, IMAP family member 5) genes on chromosome 7. Alternative splicing results in multiple readthrough transcript variants, one of which encodes a fusion protein that shares sequence identity with each individual gene product. [provided by RefSeq, Jan 2015]

GIMAP5 (HGNC:):

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 = 0.627 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GIMAP5	NM_018384.5	c.-7+677A>G		intron_variant		ENST00000358647.5	NP_060854.2
GIMAP1-GIMAP5	NM_001199577.2	c.606+677A>G		intron_variant			NP_001186506.1
GIMAP1-GIMAP5	NM_001303630.2	c.222+677A>G		intron_variant			NP_001290559.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GIMAP5	ENST00000358647.5	c.-7+677A>G		intron_variant		1	NM_018384.5	ENSP00000351473.3
GIMAP1-GIMAP5	ENST00000611999.4	c.606+677A>G		intron_variant		5		ENSP00000477920.1

Frequencies

GnomAD3 genomes AF: 0.487 AC: 73895 AN: 151826 Hom.: 18764 Cov.: 31

Gnomad AFR AF: 0.633

Gnomad AMI AF: 0.281

Gnomad AMR AF: 0.416

Gnomad ASJ AF: 0.386

Gnomad EAS AF: 0.361

Gnomad SAS AF: 0.473

Gnomad FIN AF: 0.555

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.422

Gnomad OTH AF: 0.456

GnomAD4 exome AF: 0.371 AC: 118 AN: 318 Hom.: 25 Cov.: 0 AF XY: 0.351 AC XY: 47 AN XY: 134

Gnomad4 AMR exome AF: 0.367

Gnomad4 ASJ exome AF: 0.500

Gnomad4 SAS exome AF: 0.500

Gnomad4 FIN exome AF: 0.750

Gnomad4 NFE exome AF: 0.371

Gnomad4 OTH exome AF: 0.214

GnomAD4 genome AF: 0.487 AC: 73983 AN: 151944 Hom.: 18785 Cov.: 31 AF XY: 0.492 AC XY: 36538 AN XY: 74254

Gnomad4 AFR AF: 0.633

Gnomad4 AMR AF: 0.417

Gnomad4 ASJ AF: 0.386

Gnomad4 EAS AF: 0.362

Gnomad4 SAS AF: 0.473

Gnomad4 FIN AF: 0.555

Gnomad4 NFE AF: 0.422

Gnomad4 OTH AF: 0.456

Alfa AF: 0.455 Hom.: 3198

Bravo AF: 0.479

Asia WGS AF: 0.430 AC: 1495 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	0.87
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: rs9657891; hg19: chr7-150435473;