7-150570142-T-G

Variant names:

• chr7-150570142-T-G
• rs2293174
• NM_018326.3:c.58+183T>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+183T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.166 in 613,834 control chromosomes in the GnomAD database, including 9,116 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 0.17 (2173 hom., cov: 31)
  • Exomes 𝑓: 0.17 (6943 hom.)
• Consequence: GIMAP4 NM_018326.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.02
• 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=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.235 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GIMAP4	NM_018326.3	c.58+183T>G		intron_variant	Intron 2 of 2	ENST00000255945.4	NP_060796.1
GIMAP4	NM_001363532.2	c.100+141T>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+183T>G		intron_variant	Intron 2 of 2	1	NM_018326.3	ENSP00000255945.2

Frequencies

GnomAD3 genomes AF: 0.166 AC: 25190 AN: 152026 Hom.: 2175 Cov.: 31

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.141

Gnomad ASJ AF: 0.0847

Gnomad EAS AF: 0.205

Gnomad SAS AF: 0.248

Gnomad FIN AF: 0.188

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.157

Gnomad OTH AF: 0.166

GnomAD4 exome AF: 0.167 AC: 76921 AN: 461690 Hom.: 6943 AF XY: 0.170 AC XY: 41638 AN XY: 245546

African (AFR) AF: 0.177 AC: 2310 AN: 13040

American (AMR) AF: 0.138 AC: 3131 AN: 22638

Ashkenazi Jewish (ASJ) AF: 0.0939 AC: 1348 AN: 14358

East Asian (EAS) AF: 0.204 AC: 6311 AN: 31002

South Asian (SAS) AF: 0.234 AC: 11176 AN: 47684

European-Finnish (FIN) AF: 0.177 AC: 5280 AN: 29836

Middle Eastern (MID) AF: 0.122 AC: 240 AN: 1966

European-Non Finnish (NFE) AF: 0.156 AC: 42976 AN: 274638

Other (OTH) AF: 0.156 AC: 4149 AN: 26528

GnomAD4 genome AF: 0.166 AC: 25198 AN: 152144 Hom.: 2173 Cov.: 31 AF XY: 0.167 AC XY: 12404 AN XY: 74398

African (AFR) AF: 0.176 AC: 7303 AN: 41496

American (AMR) AF: 0.141 AC: 2153 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0847 AC: 294 AN: 3470

East Asian (EAS) AF: 0.205 AC: 1059 AN: 5172

South Asian (SAS) AF: 0.247 AC: 1191 AN: 4826

European-Finnish (FIN) AF: 0.188 AC: 1994 AN: 10594

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.157 AC: 10649 AN: 67978

Other (OTH) AF: 0.167 AC: 352 AN: 2112

Alfa AF: 0.0809 Hom.: 110

Bravo AF: 0.160

Asia WGS AF: 0.238 AC: 831 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.5
DANN	Benign	0.71
PhyloP100		1.0
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: rs2293174; hg19: chr7-150267230;