chr7-150573962-C-A

Variant names:

• chr7-150573962-C-A
• rs952642
• ENST00000943245.1:c.*902C>A

Variant summary

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

The ENST00000943245.1(GIMAP4):​c.*902C>A variant causes a splice region 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 ENST00000943245.1 splice_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.43
• Publications: 3 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=-0.76).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.492 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000943245.1. 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.*902C>A		downstream_gene	N/A	NP_060796.1
	GIMAP4	NM_001363532.2		c.*902C>A		downstream_gene	N/A	NP_001350461.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GIMAP4	ENST00000943245.1		c.*902C>A		splice_region	Exon 3 of 3	ENSP00000613304.1
	GIMAP4	ENST00000943245.1		c.*902C>A		3_prime_UTR	Exon 3 of 3	ENSP00000613304.1
	GIMAP4	ENST00000255945.4	TSL:1 MANE Select	c.*902C>A		downstream_gene	N/A	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

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) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

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

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.497 AC: 20603 AN: 41414

American (AMR) AF: 0.250 AC: 3815 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.234 AC: 810 AN: 3464

East Asian (EAS) AF: 0.313 AC: 1620 AN: 5184

South Asian (SAS) AF: 0.253 AC: 1221 AN: 4820

European-Finnish (FIN) AF: 0.220 AC: 2327 AN: 10560

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.219 AC: 14866 AN: 67984

Other (OTH) AF: 0.274 AC: 578 AN: 2110

Alfa AF: 0.262 Hom.: 2324

Bravo AF: 0.313

Asia WGS AF: 0.288 AC: 1002 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	6.8
DANN	Benign	0.68
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs952642; hg19: chr7-150271050;