chr7-150470495-A-G

Position:

• chr7-150470495-A-G

Variant summary

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

The NM_175571.4(GIMAP8):​c.637-334A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.327 in 151,692 control chromosomes in the GnomAD database, including 8,235 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 0.33 (8235 hom., cov: 30)
• Consequence: GIMAP8 NM_175571.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.191

Genes affected

GIMAP8 (HGNC:21792): (GTPase, IMAP family member 8) This gene encodes a protein belonging to the GTP-binding superfamily and to the immuno-associated nucleotide (IAN) subfamily of nucleotide-binding proteins. 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=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.399 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GIMAP8	NM_175571.4	c.637-334A>G		intron_variant		ENST00000307271.4
GIMAP8	XM_005249950.5	c.637-334A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GIMAP8	ENST00000307271.4	c.637-334A>G		intron_variant		1	NM_175571.4	P1

Frequencies

GnomAD3 genomes AF: 0.327 AC: 49610 AN: 151572 Hom.: 8230 Cov.: 30

Gnomad AFR AF: 0.313

Gnomad AMI AF: 0.257

Gnomad AMR AF: 0.282

Gnomad ASJ AF: 0.398

Gnomad EAS AF: 0.415

Gnomad SAS AF: 0.263

Gnomad FIN AF: 0.287

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.347

Gnomad OTH AF: 0.325

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

GnomAD4 genome AF: 0.327 AC: 49640 AN: 151692 Hom.: 8235 Cov.: 30 AF XY: 0.323 AC XY: 23960 AN XY: 74116

Gnomad4 AFR AF: 0.313

Gnomad4 AMR AF: 0.282

Gnomad4 ASJ AF: 0.398

Gnomad4 EAS AF: 0.414

Gnomad4 SAS AF: 0.264

Gnomad4 FIN AF: 0.287

Gnomad4 NFE AF: 0.347

Gnomad4 OTH AF: 0.322

Alfa AF: 0.348 Hom.: 12659

Bravo AF: 0.333

Asia WGS AF: 0.302 AC: 1049 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.76
DANN	Benign	0.35

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: rs6969414; hg19: chr7-150167583;