rs1317276

Positions:

• chr7-150571428-C-A
• chr7-150571428-C-T

Variant summary

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

The NM_018326.3(GIMAP4):​c.59-701C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.249 in 152,036 control chromosomes in the GnomAD database, including 4,891 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 0.25 (4891 hom., cov: 32)
• Consequence: GIMAP4 NM_018326.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0180

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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.304 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GIMAP4	NM_018326.3	c.59-701C>A		intron_variant		ENST00000255945.4	NP_060796.1
GIMAP4	NM_001363532.2	c.101-701C>A		intron_variant			NP_001350461.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GIMAP4	ENST00000255945.4	c.59-701C>A		intron_variant		1	NM_018326.3	ENSP00000255945	P1

Frequencies

GnomAD3 genomes AF: 0.249 AC: 37841 AN: 151918 Hom.: 4880 Cov.: 32

Gnomad AFR AF: 0.309

Gnomad AMI AF: 0.207

Gnomad AMR AF: 0.228

Gnomad ASJ AF: 0.226

Gnomad EAS AF: 0.311

Gnomad SAS AF: 0.230

Gnomad FIN AF: 0.238

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.218

Gnomad OTH AF: 0.228

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

GnomAD4 genome AF: 0.249 AC: 37889 AN: 152036 Hom.: 4891 Cov.: 32 AF XY: 0.250 AC XY: 18597 AN XY: 74310

Gnomad4 AFR AF: 0.309

Gnomad4 AMR AF: 0.228

Gnomad4 ASJ AF: 0.226

Gnomad4 EAS AF: 0.312

Gnomad4 SAS AF: 0.230

Gnomad4 FIN AF: 0.238

Gnomad4 NFE AF: 0.218

Gnomad4 OTH AF: 0.233

Alfa AF: 0.144 Hom.: 312

Bravo AF: 0.251

Asia WGS AF: 0.259 AC: 897 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	9.6
DANN	Benign	0.65

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

Publications

LitVar

Other links and lift over

dbSNP: rs1317276; hg19: chr7-150268516;