rs11769703

Positions:

• chr7-150569747-G-A

Variant summary

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

The NM_018326.3(GIMAP4):​c.-14-141G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.229 in 584,234 control chromosomes in the GnomAD database, including 16,371 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 0.21 (3761 hom., cov: 31)
  • Exomes 𝑓: 0.24 (12610 hom.)
• Consequence: GIMAP4 NM_018326.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0760

Genes affected

GIMAP4 (HGNC:21872): (GTPase, IMAP family member 4) This gene encodes a protein belonging to the GTP-binding superfamily and to the immuno-associated nucleotide (IAN) subfamily of nucleotide-binding proteins. The encoded protein of this gene may be negatively regulated by T-cell acute lymphocytic leukemia 1 (TAL1). In humans, the IAN subfamily genes are located in a cluster at 7q36.1. [provided by RefSeq, Jul 2008]

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 (AMR) allele frequency at 95% confidence interval = 0.264 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GIMAP4	NM_018326.3	c.-14-141G>A		intron_variant		ENST00000255945.4
GIMAP4	NM_001363532.2	c.-14-141G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GIMAP4	ENST00000255945.4	c.-14-141G>A		intron_variant		1	NM_018326.3	P1

Frequencies

GnomAD3 genomes AF: 0.210 AC: 31893 AN: 151954 Hom.: 3763 Cov.: 31

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.271

Gnomad ASJ AF: 0.270

Gnomad EAS AF: 0.176

Gnomad SAS AF: 0.239

Gnomad FIN AF: 0.340

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.234

Gnomad OTH AF: 0.183

GnomAD4 exome AF: 0.235 AC: 101671 AN: 432162 Hom.: 12610 AF XY: 0.235 AC XY: 53418 AN XY: 227518

Gnomad4 AFR exome AF: 0.107

Gnomad4 AMR exome AF: 0.296

Gnomad4 ASJ exome AF: 0.263

Gnomad4 EAS exome AF: 0.180

Gnomad4 SAS exome AF: 0.240

Gnomad4 FIN exome AF: 0.329

Gnomad4 NFE exome AF: 0.230

Gnomad4 OTH exome AF: 0.233

GnomAD4 genome AF: 0.210 AC: 31900 AN: 152072 Hom.: 3761 Cov.: 31 AF XY: 0.215 AC XY: 16008 AN XY: 74326

Gnomad4 AFR AF: 0.110

Gnomad4 AMR AF: 0.271

Gnomad4 ASJ AF: 0.270

Gnomad4 EAS AF: 0.175

Gnomad4 SAS AF: 0.238

Gnomad4 FIN AF: 0.340

Gnomad4 NFE AF: 0.234

Gnomad4 OTH AF: 0.182

Alfa AF: 0.228 Hom.: 3845

Bravo AF: 0.202

Asia WGS AF: 0.212 AC: 738 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	2.6
DANN	Benign	0.37

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: rs11769703; hg19: chr7-150266835;