rs1317276

Variant names:

• chr7-150571428-C-A
• rs1317276
• NM_018326.3:c.59-701C>A

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

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

The NM_018326.3(GIMAP4):​c.59-701C>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
• 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.304 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018326.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GIMAP4	NM_018326.3	MANE Select	c.59-701C>A		intron	N/A	NP_060796.1
	GIMAP4	NM_001363532.2		c.101-701C>A		intron	N/A	NP_001350461.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GIMAP4	ENST00000255945.4	TSL:1 MANE Select	c.59-701C>A		intron	N/A	ENSP00000255945.2
	GIMAP4	ENST00000461940.5	TSL:2	c.101-701C>A		intron	N/A	ENSP00000419545.1
	GIMAP4	ENST00000479232.1	TSL:4	c.101-701C>A		intron	N/A	ENSP00000418615.1

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

African (AFR) AF: 0.309 AC: 12797 AN: 41450

American (AMR) AF: 0.228 AC: 3478 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.226 AC: 784 AN: 3464

East Asian (EAS) AF: 0.312 AC: 1615 AN: 5174

South Asian (SAS) AF: 0.230 AC: 1111 AN: 4826

European-Finnish (FIN) AF: 0.238 AC: 2515 AN: 10554

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.218 AC: 14841 AN: 67986

Other (OTH) AF: 0.233 AC: 491 AN: 2110

Alfa AF: 0.151 Hom.: 351

Bravo AF: 0.251

Asia WGS AF: 0.259 AC: 897 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	9.6
DANN	Benign	0.65
PhyloP100		0.018
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: rs1317276; hg19: chr7-150268516;