7-150470495-A-G

Variant names:

• chr7-150470495-A-G
• rs6969414
• NM_175571.4:c.637-334A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 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=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.399 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_175571.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GIMAP8	NM_175571.4	MANE Select	c.637-334A>G		intron	N/A	NP_783161.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GIMAP8	ENST00000307271.4	TSL:1 MANE Select	c.637-334A>G		intron	N/A	ENSP00000305107.3

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

African (AFR) AF: 0.313 AC: 12930 AN: 41302

American (AMR) AF: 0.282 AC: 4302 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.398 AC: 1377 AN: 3462

East Asian (EAS) AF: 0.414 AC: 2138 AN: 5166

South Asian (SAS) AF: 0.264 AC: 1265 AN: 4796

European-Finnish (FIN) AF: 0.287 AC: 3018 AN: 10502

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.347 AC: 23595 AN: 67910

Other (OTH) AF: 0.322 AC: 677 AN: 2102

Alfa AF: 0.346 Hom.: 17334

Bravo AF: 0.333

Asia WGS AF: 0.302 AC: 1049 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.76
DANN	Benign	0.35
PhyloP100		-0.19
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: rs6969414; hg19: chr7-150167583;