7-150570649-A-G

Variant names:

• chr7-150570649-A-G
• rs1317559
• NM_018326.3:c.58+690A>G

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+690A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.778 in 152,120 control chromosomes in the GnomAD database, including 46,697 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 0.78 (46697 hom., cov: 31)
• Consequence: GIMAP4 NM_018326.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.894
• Publications: 1 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 (AFR) allele frequency at 95% confidence interval = 0.91 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GIMAP4	NM_018326.3	c.58+690A>G		intron_variant	Intron 2 of 2	ENST00000255945.4	NP_060796.1
GIMAP4	NM_001363532.2	c.100+648A>G		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+690A>G		intron_variant	Intron 2 of 2	1	NM_018326.3	ENSP00000255945.2

Frequencies

GnomAD3 genomes AF: 0.778 AC: 118258 AN: 152002 Hom.: 46642 Cov.: 31

Gnomad AFR AF: 0.917

Gnomad AMI AF: 0.713

Gnomad AMR AF: 0.737

Gnomad ASJ AF: 0.674

Gnomad EAS AF: 0.799

Gnomad SAS AF: 0.794

Gnomad FIN AF: 0.828

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.700

Gnomad OTH AF: 0.728

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

GnomAD4 genome AF: 0.778 AC: 118372 AN: 152120 Hom.: 46697 Cov.: 31 AF XY: 0.784 AC XY: 58283 AN XY: 74382

African (AFR) AF: 0.917 AC: 38086 AN: 41514

American (AMR) AF: 0.737 AC: 11265 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.674 AC: 2339 AN: 3470

East Asian (EAS) AF: 0.800 AC: 4130 AN: 5164

South Asian (SAS) AF: 0.794 AC: 3825 AN: 4820

European-Finnish (FIN) AF: 0.828 AC: 8763 AN: 10586

Middle Eastern (MID) AF: 0.673 AC: 198 AN: 294

European-Non Finnish (NFE) AF: 0.700 AC: 47576 AN: 67966

Other (OTH) AF: 0.731 AC: 1540 AN: 2106

Alfa AF: 0.729 Hom.: 13885

Bravo AF: 0.775

Asia WGS AF: 0.828 AC: 2879 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.30
DANN	Benign	0.68
PhyloP100		-0.89
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: rs1317559; hg19: chr7-150267737;