7-150738355-C-T

Position:

• chr7-150738355-C-T

Variant summary

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

The ENST00000358647.5(GIMAP5):​c.-7+647C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.376 in 152,480 control chromosomes in the GnomAD database, including 11,761 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 0.38 (11736 hom., cov: 31)
  • Exomes 𝑓: 0.31 (25 hom.)
• Consequence: GIMAP5 ENST00000358647.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08

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 = 0.534 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GIMAP5	NM_018384.5	c.-7+647C>T		intron_variant		ENST00000358647.5	NP_060854.2
GIMAP1-GIMAP5	NM_001199577.2	c.606+647C>T		intron_variant			NP_001186506.1
GIMAP1-GIMAP5	NM_001303630.2	c.222+647C>T		intron_variant			NP_001290559.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GIMAP5	ENST00000358647.5	c.-7+647C>T		intron_variant		1	NM_018384.5	ENSP00000351473	P1

Frequencies

GnomAD3 genomes AF: 0.376 AC: 57139 AN: 151788 Hom.: 11719 Cov.: 31

Gnomad AFR AF: 0.540

Gnomad AMI AF: 0.164

Gnomad AMR AF: 0.282

Gnomad ASJ AF: 0.336

Gnomad EAS AF: 0.273

Gnomad SAS AF: 0.375

Gnomad FIN AF: 0.401

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.308

Gnomad OTH AF: 0.346

GnomAD4 exome AF: 0.314 AC: 180 AN: 574 Hom.: 25 Cov.: 0 AF XY: 0.343 AC XY: 96 AN XY: 280

Gnomad4 AFR exome AF: 0.500

Gnomad4 AMR exome AF: 0.289

Gnomad4 ASJ exome AF: 0.500

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.250

Gnomad4 FIN exome AF: 0.250

Gnomad4 NFE exome AF: 0.314

Gnomad4 OTH exome AF: 0.400

GnomAD4 genome AF: 0.377 AC: 57205 AN: 151906 Hom.: 11736 Cov.: 31 AF XY: 0.379 AC XY: 28110 AN XY: 74208

Gnomad4 AFR AF: 0.540

Gnomad4 AMR AF: 0.281

Gnomad4 ASJ AF: 0.336

Gnomad4 EAS AF: 0.273

Gnomad4 SAS AF: 0.375

Gnomad4 FIN AF: 0.401

Gnomad4 NFE AF: 0.308

Gnomad4 OTH AF: 0.348

Alfa AF: 0.231 Hom.: 558

Bravo AF: 0.372

Asia WGS AF: 0.331 AC: 1154 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	4.1
DANN	Benign	0.49

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: rs9657890; hg19: chr7-150435443;