rs952642

Variant names:

• chr7-150573962-C-A
• rs952642
• NM_018326.3:c.*902C>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_018326.3(GIMAP4):​c.*902C>A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.303 in 152,012 control chromosomes in the GnomAD database, including 8,161 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 0.30 (8161 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: GIMAP4 NM_018326.3 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.43

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.492 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GIMAP4	NM_018326.3	c.*902C>A		downstream_gene_variant		ENST00000255945.4	NP_060796.1
GIMAP4	NM_001363532.2	c.*902C>A		downstream_gene_variant			NP_001350461.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GIMAP4	ENST00000255945.4	c.*902C>A		downstream_gene_variant		1	NM_018326.3	ENSP00000255945.2

Frequencies

GnomAD3 genomes AF: 0.303 AC: 46060 AN: 151894 Hom.: 8150 Cov.: 32

Gnomad AFR AF: 0.498

Gnomad AMI AF: 0.214

Gnomad AMR AF: 0.250

Gnomad ASJ AF: 0.234

Gnomad EAS AF: 0.312

Gnomad SAS AF: 0.253

Gnomad FIN AF: 0.220

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.219

Gnomad OTH AF: 0.271

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.303 AC: 46121 AN: 152012 Hom.: 8161 Cov.: 32 AF XY: 0.303 AC XY: 22521 AN XY: 74300

Gnomad4 AFR AF: 0.497

Gnomad4 AMR AF: 0.250

Gnomad4 ASJ AF: 0.234

Gnomad4 EAS AF: 0.313

Gnomad4 SAS AF: 0.253

Gnomad4 FIN AF: 0.220

Gnomad4 NFE AF: 0.219

Gnomad4 OTH AF: 0.274

Alfa AF: 0.257 Hom.: 1774

Bravo AF: 0.313

Asia WGS AF: 0.288 AC: 1002 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	6.8
DANN	Benign	0.68

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs952642; hg19: chr7-150271050;