rs2373816

Variant names:

• chr7-150574041-G-A
• rs2373816
• NM_018326.3:c.*981G>A

Your query was ambiguous. Multiple possible variants found:

• chr7-150574041-G-A
• chr7-150574041-G-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.*981G>A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.709 in 152,028 control chromosomes in the GnomAD database, including 39,335 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 0.71 (39334 hom., cov: 31)
  • Exomes 𝑓: 1.0 (1 hom.)
• Consequence: GIMAP4 NM_018326.3 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0570
• 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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.879 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GIMAP4	NM_018326.3	MANE Select	c.*981G>A		downstream_gene	N/A	NP_060796.1	Q9NUV9
	GIMAP4	NM_001363532.2		c.*981G>A		downstream_gene	N/A	NP_001350461.1	G5E9W9

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GIMAP4	ENST00000255945.4	TSL:1 MANE Select	c.*981G>A		downstream_gene	N/A	ENSP00000255945.2	Q9NUV9
	GIMAP4	ENST00000851189.1		c.*981G>A		downstream_gene	N/A	ENSP00000521248.1
	GIMAP4	ENST00000851190.1		c.*981G>A		downstream_gene	N/A	ENSP00000521249.1

Frequencies

GnomAD3 genomes AF: 0.709 AC: 107743 AN: 151906 Hom.: 39291 Cov.: 31

Gnomad AFR AF: 0.886

Gnomad AMI AF: 0.675

Gnomad AMR AF: 0.677

Gnomad ASJ AF: 0.591

Gnomad EAS AF: 0.698

Gnomad SAS AF: 0.728

Gnomad FIN AF: 0.749

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.611

Gnomad OTH AF: 0.645

GnomAD4 exome AF: 1.00 AC: 2 AN: 2 Hom.: 1 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 1.00 AC: 2 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.709 AC: 107842 AN: 152026 Hom.: 39334 Cov.: 31 AF XY: 0.715 AC XY: 53089 AN XY: 74296

African (AFR) AF: 0.886 AC: 36780 AN: 41498

American (AMR) AF: 0.677 AC: 10326 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.591 AC: 2050 AN: 3468

East Asian (EAS) AF: 0.699 AC: 3610 AN: 5168

South Asian (SAS) AF: 0.727 AC: 3506 AN: 4822

European-Finnish (FIN) AF: 0.749 AC: 7911 AN: 10558

Middle Eastern (MID) AF: 0.622 AC: 183 AN: 294

European-Non Finnish (NFE) AF: 0.611 AC: 41491 AN: 67934

Other (OTH) AF: 0.648 AC: 1369 AN: 2112

Alfa AF: 0.651 Hom.: 19740

Bravo AF: 0.711

Asia WGS AF: 0.751 AC: 2612 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.0
DANN	Benign	0.31
PhyloP100		-0.057
Mutation Taster		=92/8	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs2373816; hg19: chr7-150271129;