chr7-150463370-G-A

Variant names:

• chr7-150463370-G-A
• rs11769211
• NM_175571.4:c.-28-3301G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
GIMAP8	NM_175571.4	c.-28-3301G>A		intron_variant	Intron 1 of 4	ENST00000307271.4	NP_783161.1
GIMAP8	XM_005249950.5	c.-28-3301G>A		intron_variant	Intron 2 of 5		XP_005250007.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GIMAP8	ENST00000307271.4	c.-28-3301G>A		intron_variant	Intron 1 of 4	1	NM_175571.4	ENSP00000305107.3

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

African (AFR) AF: 0.166 AC: 6859 AN: 41432

American (AMR) AF: 0.268 AC: 4094 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.396 AC: 1374 AN: 3470

East Asian (EAS) AF: 0.413 AC: 2134 AN: 5162

South Asian (SAS) AF: 0.232 AC: 1115 AN: 4812

European-Finnish (FIN) AF: 0.288 AC: 3033 AN: 10518

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.347 AC: 23577 AN: 67926

Other (OTH) AF: 0.287 AC: 605 AN: 2108

Alfa AF: 0.334 Hom.: 14639

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
PhyloP100		0.34
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs11769211; hg19: chr7-150160458; COSMIC: COSV107314883;