NM_018326.3:c.59-57G>T

Variant names:

• chr7-150572072-G-T
• rs7806724
• NM_018326.3:c.59-57G>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.59-57G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.226 in 1,129,688 control chromosomes in the GnomAD database, including 29,644 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 (4863 hom., cov: 32)
  • Exomes 𝑓: 0.22 (24781 hom.)
• Consequence: GIMAP4 NM_018326.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23
• Publications: 5 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 (AFR) allele frequency at 95% confidence interval = 0.304 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GIMAP4	NM_018326.3	c.59-57G>T		intron_variant	Intron 2 of 2	ENST00000255945.4	NP_060796.1
GIMAP4	NM_001363532.2	c.101-57G>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.59-57G>T		intron_variant	Intron 2 of 2	1	NM_018326.3	ENSP00000255945.2

Frequencies

GnomAD3 genomes AF: 0.248 AC: 37710 AN: 151804 Hom.: 4852 Cov.: 32

Gnomad AFR AF: 0.309

Gnomad AMI AF: 0.207

Gnomad AMR AF: 0.227

Gnomad ASJ AF: 0.225

Gnomad EAS AF: 0.297

Gnomad SAS AF: 0.229

Gnomad FIN AF: 0.238

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.218

Gnomad OTH AF: 0.227

GnomAD4 exome AF: 0.223 AC: 217580 AN: 977768 Hom.: 24781 AF XY: 0.223 AC XY: 111229 AN XY: 499568

African (AFR) AF: 0.307 AC: 7081 AN: 23064

American (AMR) AF: 0.207 AC: 7025 AN: 33858

Ashkenazi Jewish (ASJ) AF: 0.224 AC: 4270 AN: 19058

East Asian (EAS) AF: 0.310 AC: 11612 AN: 37426

South Asian (SAS) AF: 0.223 AC: 14372 AN: 64508

European-Finnish (FIN) AF: 0.228 AC: 10065 AN: 44148

Middle Eastern (MID) AF: 0.226 AC: 1062 AN: 4690

European-Non Finnish (NFE) AF: 0.216 AC: 152432 AN: 707156

Other (OTH) AF: 0.220 AC: 9661 AN: 43860

GnomAD4 genome AF: 0.249 AC: 37758 AN: 151920 Hom.: 4863 Cov.: 32 AF XY: 0.250 AC XY: 18524 AN XY: 74232

African (AFR) AF: 0.309 AC: 12785 AN: 41402

American (AMR) AF: 0.227 AC: 3472 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.225 AC: 782 AN: 3468

East Asian (EAS) AF: 0.298 AC: 1536 AN: 5158

South Asian (SAS) AF: 0.230 AC: 1107 AN: 4822

European-Finnish (FIN) AF: 0.238 AC: 2515 AN: 10546

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

European-Non Finnish (NFE) AF: 0.218 AC: 14815 AN: 67928

Other (OTH) AF: 0.232 AC: 489 AN: 2108

Alfa AF: 0.235 Hom.: 687

Bravo AF: 0.251

Asia WGS AF: 0.250 AC: 868 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	0.44
DANN	Benign	0.63
PhyloP100		-1.2
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: rs7806724; hg19: chr7-150269160;