rs13235400

chr7-150741242-G-Achr7-150741242-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.43+315G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.531 in 151,300 control chromosomes in the GnomAD database, including 23,314 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 0.53 (23314 hom., cov: 31)
• Consequence: GIMAP5 NM_018384.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.214

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.779 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GIMAP5	NM_018384.5	c.43+315G>A		intron_variant		ENST00000358647.5
GIMAP1-GIMAP5	NM_001199577.2	c.655+315G>A		intron_variant
GIMAP1-GIMAP5	NM_001303630.2	c.271+315G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GIMAP5	ENST00000358647.5	c.43+315G>A		intron_variant		1	NM_018384.5	P1

Frequencies

GnomAD3 genomes AF: 0.531 AC: 80262 AN: 151184 Hom.: 23272 Cov.: 31

Gnomad AFR AF: 0.786

Gnomad AMI AF: 0.280

Gnomad AMR AF: 0.432

Gnomad ASJ AF: 0.397

Gnomad EAS AF: 0.373

Gnomad SAS AF: 0.495

Gnomad FIN AF: 0.550

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.422

Gnomad OTH AF: 0.488

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

GnomAD4 genome AF: 0.531 AC: 80375 AN: 151300 Hom.: 23314 Cov.: 31 AF XY: 0.535 AC XY: 39520 AN XY: 73900

Gnomad4 AFR AF: 0.786

Gnomad4 AMR AF: 0.432

Gnomad4 ASJ AF: 0.397

Gnomad4 EAS AF: 0.374

Gnomad4 SAS AF: 0.495

Gnomad4 FIN AF: 0.550

Gnomad4 NFE AF: 0.422

Gnomad4 OTH AF: 0.489

Alfa AF: 0.403 Hom.: 1793

Bravo AF: 0.532

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.0
Dann	Benign	0.35

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: rs13235400; hg19: chr7-150438330;