rs11769211

Positions:

• chr7-150463370-G-A
• chr7-150463370-G-C

Variant summary

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

The NM_175571.4(GIMAP8):​c.-28-3301G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.284 in 151,912 control chromosomes in the GnomAD database, including 6,620 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 0.28 (6620 hom., cov: 32)
• Consequence: GIMAP8 NM_175571.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.335

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=-0.9).
• 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.-28-3301G>A		intron_variant		ENST00000307271.4
GIMAP8	XM_005249950.5	c.-28-3301G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GIMAP8	ENST00000307271.4	c.-28-3301G>A		intron_variant		1	NM_175571.4	P1

Frequencies

GnomAD3 genomes AF: 0.284 AC: 43110 AN: 151794 Hom.: 6616 Cov.: 32

Gnomad AFR AF: 0.165

Gnomad AMI AF: 0.256

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.396

Gnomad EAS AF: 0.414

Gnomad SAS AF: 0.231

Gnomad FIN AF: 0.288

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.347

Gnomad OTH AF: 0.290

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

GnomAD4 genome AF: 0.284 AC: 43126 AN: 151912 Hom.: 6620 Cov.: 32 AF XY: 0.281 AC XY: 20849 AN XY: 74266

Gnomad4 AFR AF: 0.166

Gnomad4 AMR AF: 0.268

Gnomad4 ASJ AF: 0.396

Gnomad4 EAS AF: 0.413

Gnomad4 SAS AF: 0.232

Gnomad4 FIN AF: 0.288

Gnomad4 NFE AF: 0.347

Gnomad4 OTH AF: 0.287

Alfa AF: 0.340 Hom.: 11907

Bravo AF: 0.284

Asia WGS AF: 0.275 AC: 953 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.1
DANN	Benign	0.49

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: rs11769211; hg19: chr7-150160458;