7-150569747-G-A

Variant names:

• chr7-150569747-G-A
• rs11769703
• NM_018326.3:c.-14-141G>A

Variant summary

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

The NM_018326.3(GIMAP4):​c.-14-141G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.229 in 584,234 control chromosomes in the GnomAD database, including 16,371 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 0.21 (3761 hom., cov: 31)
  • Exomes 𝑓: 0.24 (12610 hom.)
• Consequence: GIMAP4 NM_018326.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0760
• 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.264 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GIMAP4	NM_018326.3	c.-14-141G>A		intron_variant	Intron 1 of 2	ENST00000255945.4	NP_060796.1
GIMAP4	NM_001363532.2	c.-14-141G>A		intron_variant	Intron 1 of 2		NP_001350461.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GIMAP4	ENST00000255945.4	c.-14-141G>A		intron_variant	Intron 1 of 2	1	NM_018326.3	ENSP00000255945.2

Frequencies

GnomAD3 genomes AF: 0.210 AC: 31893 AN: 151954 Hom.: 3763 Cov.: 31

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.271

Gnomad ASJ AF: 0.270

Gnomad EAS AF: 0.176

Gnomad SAS AF: 0.239

Gnomad FIN AF: 0.340

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.234

Gnomad OTH AF: 0.183

GnomAD4 exome AF: 0.235 AC: 101671 AN: 432162 Hom.: 12610 AF XY: 0.235 AC XY: 53418 AN XY: 227518

African (AFR) AF: 0.107 AC: 1288 AN: 12046

American (AMR) AF: 0.296 AC: 5319 AN: 17954

Ashkenazi Jewish (ASJ) AF: 0.263 AC: 3468 AN: 13188

East Asian (EAS) AF: 0.180 AC: 5357 AN: 29762

South Asian (SAS) AF: 0.240 AC: 9854 AN: 41040

European-Finnish (FIN) AF: 0.329 AC: 10713 AN: 32570

Middle Eastern (MID) AF: 0.174 AC: 613 AN: 3522

European-Non Finnish (NFE) AF: 0.230 AC: 59189 AN: 256902

Other (OTH) AF: 0.233 AC: 5870 AN: 25178

GnomAD4 genome AF: 0.210 AC: 31900 AN: 152072 Hom.: 3761 Cov.: 31 AF XY: 0.215 AC XY: 16008 AN XY: 74326

African (AFR) AF: 0.110 AC: 4556 AN: 41476

American (AMR) AF: 0.271 AC: 4141 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.270 AC: 937 AN: 3472

East Asian (EAS) AF: 0.175 AC: 908 AN: 5174

South Asian (SAS) AF: 0.238 AC: 1148 AN: 4816

European-Finnish (FIN) AF: 0.340 AC: 3590 AN: 10546

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.234 AC: 15923 AN: 67984

Other (OTH) AF: 0.182 AC: 384 AN: 2114

Alfa AF: 0.224 Hom.: 4991

Bravo AF: 0.202

Asia WGS AF: 0.212 AC: 738 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.6
DANN	Benign	0.37
PhyloP100		-0.076
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: rs11769703; hg19: chr7-150266835;