NM_018326.3:c.58+1051G>T

Variant names:

• chr7-150571010-G-T
• rs9640279
• NM_018326.3:c.58+1051G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_018326.3(GIMAP4):​c.58+1051G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.249 in 151,972 control chromosomes in the GnomAD database, including 4,899 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 0.25 (4899 hom., cov: 31)
• Consequence: GIMAP4 NM_018326.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.379
• Publications: 7 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.305 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GIMAP4	NM_018326.3	c.58+1051G>T		intron_variant	Intron 2 of 2	ENST00000255945.4	NP_060796.1
GIMAP4	NM_001363532.2	c.100+1009G>T		intron_variant	Intron 2 of 2		NP_001350461.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GIMAP4	ENST00000255945.4	c.58+1051G>T		intron_variant	Intron 2 of 2	1	NM_018326.3	ENSP00000255945.2

Frequencies

GnomAD3 genomes AF: 0.249 AC: 37836 AN: 151854 Hom.: 4888 Cov.: 31

Gnomad AFR AF: 0.309

Gnomad AMI AF: 0.207

Gnomad AMR AF: 0.228

Gnomad ASJ AF: 0.226

Gnomad EAS AF: 0.311

Gnomad SAS AF: 0.229

Gnomad FIN AF: 0.238

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.218

Gnomad OTH AF: 0.228

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

GnomAD4 genome AF: 0.249 AC: 37885 AN: 151972 Hom.: 4899 Cov.: 31 AF XY: 0.250 AC XY: 18596 AN XY: 74282

African (AFR) AF: 0.309 AC: 12805 AN: 41432

American (AMR) AF: 0.228 AC: 3486 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.226 AC: 786 AN: 3472

East Asian (EAS) AF: 0.313 AC: 1614 AN: 5164

South Asian (SAS) AF: 0.230 AC: 1105 AN: 4804

European-Finnish (FIN) AF: 0.238 AC: 2517 AN: 10558

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.218 AC: 14824 AN: 67936

Other (OTH) AF: 0.232 AC: 491 AN: 2112

Alfa AF: 0.229 Hom.: 17264

Bravo AF: 0.251

Asia WGS AF: 0.259 AC: 897 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	1.8
DANN	Benign	0.59
PhyloP100		-0.38
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs9640279; hg19: chr7-150268098;