chr7-150571999-G-C

Variant names:

• chr7-150571999-G-C
• rs13242186
• NM_018326.3:c.59-130G>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.59-130G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.14 in 632,992 control chromosomes in the GnomAD database, including 6,853 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 (1358 hom., cov: 32)
  • Exomes 𝑓: 0.15 (5495 hom.)
• Consequence: GIMAP4 NM_018326.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.930
• 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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.162 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GIMAP4	NM_018326.3	c.59-130G>C		intron_variant	Intron 2 of 2	ENST00000255945.4	NP_060796.1
GIMAP4	NM_001363532.2	c.101-130G>C		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.59-130G>C		intron_variant	Intron 2 of 2	1	NM_018326.3	ENSP00000255945.2

Frequencies

GnomAD3 genomes AF: 0.121 AC: 18451 AN: 152080 Hom.: 1361 Cov.: 32

Gnomad AFR AF: 0.0479

Gnomad AMI AF: 0.184

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.0841

Gnomad EAS AF: 0.171

Gnomad SAS AF: 0.102

Gnomad FIN AF: 0.188

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.135

GnomAD4 exome AF: 0.146 AC: 70113 AN: 480794 Hom.: 5495 AF XY: 0.143 AC XY: 36507 AN XY: 254474

African (AFR) AF: 0.0460 AC: 614 AN: 13354

American (AMR) AF: 0.108 AC: 2100 AN: 19406

Ashkenazi Jewish (ASJ) AF: 0.0938 AC: 1309 AN: 13952

East Asian (EAS) AF: 0.170 AC: 5505 AN: 32424

South Asian (SAS) AF: 0.104 AC: 4730 AN: 45570

European-Finnish (FIN) AF: 0.179 AC: 5808 AN: 32368

Middle Eastern (MID) AF: 0.104 AC: 343 AN: 3298

European-Non Finnish (NFE) AF: 0.157 AC: 45927 AN: 293124

Other (OTH) AF: 0.138 AC: 3777 AN: 27298

GnomAD4 genome AF: 0.121 AC: 18451 AN: 152198 Hom.: 1358 Cov.: 32 AF XY: 0.122 AC XY: 9045 AN XY: 74404

African (AFR) AF: 0.0477 AC: 1983 AN: 41558

American (AMR) AF: 0.113 AC: 1733 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0841 AC: 292 AN: 3472

East Asian (EAS) AF: 0.171 AC: 884 AN: 5164

South Asian (SAS) AF: 0.102 AC: 492 AN: 4826

European-Finnish (FIN) AF: 0.188 AC: 1989 AN: 10580

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

European-Non Finnish (NFE) AF: 0.156 AC: 10591 AN: 67994

Other (OTH) AF: 0.137 AC: 288 AN: 2104

Alfa AF: 0.134 Hom.: 187

Bravo AF: 0.112

Asia WGS AF: 0.152 AC: 533 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.2
DANN	Benign	0.51
PhyloP100		-0.93
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: rs13242186; hg19: chr7-150269087;