7-150567515-C-T

Position:

• chr7-150567515-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.-15+78C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.084 in 152,050 control chromosomes in the GnomAD database, including 1,661 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 0.084 (1661 hom., cov: 31)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: GIMAP4 NM_018326.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.328

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]

GIMAP4 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.272 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GIMAP4	NM_018326.3	c.-15+78C>T		intron_variant		ENST00000255945.4	NP_060796.1
GIMAP4	NM_001363532.2	c.-15+78C>T		intron_variant			NP_001350461.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GIMAP4	ENST00000255945.4	c.-15+78C>T		intron_variant		1	NM_018326.3	ENSP00000255945.2

Frequencies

GnomAD3 genomes AF: 0.0839 AC: 12744 AN: 151932 Hom.: 1654 Cov.: 31

Gnomad AFR AF: 0.277

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0345

Gnomad ASJ AF: 0.0133

Gnomad EAS AF: 0.0504

Gnomad SAS AF: 0.0286

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.00284

Gnomad OTH AF: 0.0666

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 16 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 12

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0840 AC: 12776 AN: 152050 Hom.: 1661 Cov.: 31 AF XY: 0.0830 AC XY: 6171 AN XY: 74330

Gnomad4 AFR AF: 0.277

Gnomad4 AMR AF: 0.0345

Gnomad4 ASJ AF: 0.0133

Gnomad4 EAS AF: 0.0503

Gnomad4 SAS AF: 0.0283

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00284

Gnomad4 OTH AF: 0.0659

Alfa AF: 0.0134 Hom.: 169

Bravo AF: 0.0945

Asia WGS AF: 0.0610 AC: 213 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.0
DANN	Benign	0.74

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: rs6464084; hg19: chr7-150264603; COSMIC: COSV104551348;