chr7-150741711-G-T

Variant names:

• chr7-150741711-G-T
• rs9657900
• NM_018384.5:c.44-472G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_018384.5(GIMAP5):​c.44-472G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.352 in 152,122 control chromosomes in the GnomAD database, including 9,950 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 0.35 (9950 hom., cov: 32)
• Consequence: GIMAP5 NM_018384.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.05
• Publications: 10 publications found

Genes affected

GIMAP5 (HGNC:18005): (GTPase, IMAP family member 5) 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. This gene encodes an antiapoptotic protein that functions in T-cell survival. Polymorphisms in this gene are associated with systemic lupus erythematosus. Read-through transcription exists between this gene and the neighboring upstream GIMAP1 (GTPase, IMAP family member 1) gene. [provided by RefSeq, Dec 2010]

GIMAP1-GIMAP5 (HGNC:51257): (GIMAP1-GIMAP5 readthrough) This locus represents naturally occurring readthrough transcription between the neighboring GIMAP1 (GTPase, IMAP family member 1) and GIMAP5 (GTPase, IMAP family member 5) genes on chromosome 7. Alternative splicing results in multiple readthrough transcript variants, one of which encodes a fusion protein that shares sequence identity with each individual gene product. [provided by RefSeq, Jan 2015]

ACMG classification

Our verdict: Benign. The variant received -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 = 0.46 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GIMAP5	NM_018384.5	c.44-472G>T		intron_variant	Intron 2 of 2	ENST00000358647.5	NP_060854.2
GIMAP1-GIMAP5	NM_001199577.2	c.656-472G>T		intron_variant	Intron 5 of 5		NP_001186506.1
GIMAP1-GIMAP5	NM_001303630.2	c.272-472G>T		intron_variant	Intron 4 of 4		NP_001290559.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GIMAP5	ENST00000358647.5	c.44-472G>T		intron_variant	Intron 2 of 2	1	NM_018384.5	ENSP00000351473.3
GIMAP1-GIMAP5	ENST00000611999.4	c.656-472G>T		intron_variant	Intron 5 of 5	5		ENSP00000477920.1

Frequencies

GnomAD3 genomes AF: 0.352 AC: 53452 AN: 152004 Hom.: 9932 Cov.: 32

Gnomad AFR AF: 0.465

Gnomad AMI AF: 0.163

Gnomad AMR AF: 0.275

Gnomad ASJ AF: 0.343

Gnomad EAS AF: 0.283

Gnomad SAS AF: 0.264

Gnomad FIN AF: 0.400

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.307

Gnomad OTH AF: 0.332

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

GnomAD4 genome AF: 0.352 AC: 53517 AN: 152122 Hom.: 9950 Cov.: 32 AF XY: 0.354 AC XY: 26299 AN XY: 74368

African (AFR) AF: 0.465 AC: 19298 AN: 41478

American (AMR) AF: 0.274 AC: 4195 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.343 AC: 1190 AN: 3468

East Asian (EAS) AF: 0.284 AC: 1467 AN: 5164

South Asian (SAS) AF: 0.265 AC: 1280 AN: 4824

European-Finnish (FIN) AF: 0.400 AC: 4233 AN: 10588

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.307 AC: 20894 AN: 67982

Other (OTH) AF: 0.334 AC: 706 AN: 2116

Alfa AF: 0.339 Hom.: 1890

Bravo AF: 0.348

Asia WGS AF: 0.290 AC: 1009 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	6.2
DANN	Benign	0.61
PhyloP100		1.0
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: rs9657900; hg19: chr7-150438799;