7-150570142-T-G

Position:

• chr7-150570142-T-G

Variant summary

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

The NM_018326.3(GIMAP4):​c.58+183T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.166 in 613,834 control chromosomes in the GnomAD database, including 9,116 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 0.17 (2173 hom., cov: 31)
  • Exomes 𝑓: 0.17 (6943 hom.)
• Consequence: GIMAP4 NM_018326.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.02

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=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.235 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GIMAP4	NM_018326.3	c.58+183T>G		intron_variant		ENST00000255945.4	NP_060796.1
GIMAP4	NM_001363532.2	c.100+141T>G		intron_variant			NP_001350461.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GIMAP4	ENST00000255945.4	c.58+183T>G		intron_variant		1	NM_018326.3	ENSP00000255945	P1

Frequencies

GnomAD3 genomes AF: 0.166 AC: 25190 AN: 152026 Hom.: 2175 Cov.: 31

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.141

Gnomad ASJ AF: 0.0847

Gnomad EAS AF: 0.205

Gnomad SAS AF: 0.248

Gnomad FIN AF: 0.188

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.157

Gnomad OTH AF: 0.166

GnomAD4 exome AF: 0.167 AC: 76921 AN: 461690 Hom.: 6943 AF XY: 0.170 AC XY: 41638 AN XY: 245546

Gnomad4 AFR exome AF: 0.177

Gnomad4 AMR exome AF: 0.138

Gnomad4 ASJ exome AF: 0.0939

Gnomad4 EAS exome AF: 0.204

Gnomad4 SAS exome AF: 0.234

Gnomad4 FIN exome AF: 0.177

Gnomad4 NFE exome AF: 0.156

Gnomad4 OTH exome AF: 0.156

GnomAD4 genome AF: 0.166 AC: 25198 AN: 152144 Hom.: 2173 Cov.: 31 AF XY: 0.167 AC XY: 12404 AN XY: 74398

Gnomad4 AFR AF: 0.176

Gnomad4 AMR AF: 0.141

Gnomad4 ASJ AF: 0.0847

Gnomad4 EAS AF: 0.205

Gnomad4 SAS AF: 0.247

Gnomad4 FIN AF: 0.188

Gnomad4 NFE AF: 0.157

Gnomad4 OTH AF: 0.167

Alfa AF: 0.0758 Hom.: 95

Bravo AF: 0.160

Asia WGS AF: 0.238 AC: 831 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.5
DANN	Benign	0.71

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: rs2293174; hg19: chr7-150267230;