rs2373815

Variant names:

• chr7-150568387-T-C
• rs2373815
• NM_018326.3:c.-15+950T>C

Variant summary

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

The NM_018326.3(GIMAP4):​c.-15+950T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.124 in 152,282 control chromosomes in the GnomAD database, including 1,423 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 0.12 (1423 hom., cov: 32)
• Consequence: GIMAP4 NM_018326.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10
• Publications: 0 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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.195 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018326.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GIMAP4	NM_018326.3	MANE Select	c.-15+950T>C		intron	N/A	NP_060796.1
	GIMAP4	NM_001363532.2		c.-15+950T>C		intron	N/A	NP_001350461.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GIMAP4	ENST00000255945.4	TSL:1 MANE Select	c.-15+950T>C		intron	N/A	ENSP00000255945.2
	GIMAP4	ENST00000461940.5	TSL:2	c.-15+950T>C		intron	N/A	ENSP00000419545.1
	GIMAP4	ENST00000479232.1	TSL:4	c.-15+867T>C		intron	N/A	ENSP00000418615.1

Frequencies

GnomAD3 genomes AF: 0.125 AC: 18957 AN: 152164 Hom.: 1426 Cov.: 32

Gnomad AFR AF: 0.0485

Gnomad AMI AF: 0.184

Gnomad AMR AF: 0.125

Gnomad ASJ AF: 0.0841

Gnomad EAS AF: 0.205

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.188

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.141

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

GnomAD4 genome AF: 0.124 AC: 18959 AN: 152282 Hom.: 1423 Cov.: 32 AF XY: 0.125 AC XY: 9322 AN XY: 74452

African (AFR) AF: 0.0483 AC: 2009 AN: 41580

American (AMR) AF: 0.125 AC: 1909 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0841 AC: 292 AN: 3470

East Asian (EAS) AF: 0.205 AC: 1062 AN: 5178

South Asian (SAS) AF: 0.119 AC: 577 AN: 4830

European-Finnish (FIN) AF: 0.188 AC: 1985 AN: 10576

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.156 AC: 10624 AN: 68030

Other (OTH) AF: 0.143 AC: 302 AN: 2116

Alfa AF: 0.133 Hom.: 191

Bravo AF: 0.116

Asia WGS AF: 0.173 AC: 605 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.94
DANN	Benign	0.48
PhyloP100		-1.1
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: rs2373815; hg19: chr7-150265475;