NM_018326.3:c.-15+846G>T

Variant names:

• chr7-150568283-G-T
• rs2373814
• NM_018326.3:c.-15+846G>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.-15+846G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.415 in 151,968 control chromosomes in the GnomAD database, including 13,414 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 0.42 (13414 hom., cov: 32)
• Consequence: GIMAP4 NM_018326.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.201
• Publications: 2 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.503 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+846G>T		intron	N/A	NP_060796.1
	GIMAP4	NM_001363532.2		c.-15+846G>T		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+846G>T		intron	N/A	ENSP00000255945.2
	GIMAP4	ENST00000851189.1		c.-689G>T		5_prime_UTR	Exon 2 of 4	ENSP00000521248.1
	GIMAP4	ENST00000461940.5	TSL:2	c.-15+846G>T		intron	N/A	ENSP00000419545.1

Frequencies

GnomAD3 genomes AF: 0.415 AC: 63068 AN: 151850 Hom.: 13395 Cov.: 32

Gnomad AFR AF: 0.486

Gnomad AMI AF: 0.392

Gnomad AMR AF: 0.368

Gnomad ASJ AF: 0.311

Gnomad EAS AF: 0.518

Gnomad SAS AF: 0.478

Gnomad FIN AF: 0.428

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.375

Gnomad OTH AF: 0.394

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

GnomAD4 genome AF: 0.415 AC: 63131 AN: 151968 Hom.: 13414 Cov.: 32 AF XY: 0.418 AC XY: 31007 AN XY: 74248

African (AFR) AF: 0.486 AC: 20142 AN: 41434

American (AMR) AF: 0.368 AC: 5615 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.311 AC: 1079 AN: 3470

East Asian (EAS) AF: 0.519 AC: 2678 AN: 5160

South Asian (SAS) AF: 0.477 AC: 2302 AN: 4822

European-Finnish (FIN) AF: 0.428 AC: 4505 AN: 10532

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.375 AC: 25503 AN: 67962

Other (OTH) AF: 0.400 AC: 845 AN: 2112

Alfa AF: 0.388 Hom.: 2273

Bravo AF: 0.412

Asia WGS AF: 0.497 AC: 1729 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.6
DANN	Benign	0.24
PhyloP100		0.20
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: rs2373814; hg19: chr7-150265371;