7-150738385-A-G

Variant names:

• chr7-150738385-A-G
• rs9657891
• ENST00000476324.1:n.776A>G

Variant summary

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

The ENST00000476324.1(GIMAP5):​n.776A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.487 in 152,262 control chromosomes in the GnomAD database, including 18,810 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 0.49 (18785 hom., cov: 31)
  • Exomes 𝑓: 0.37 (25 hom.)
• Consequence: GIMAP5 ENST00000476324.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.644
• Publications: 1 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.627 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000476324.1. 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
	GIMAP5	NM_018384.5	MANE Select	c.-7+677A>G		intron	N/A	NP_060854.2
	GIMAP1-GIMAP5	NM_001199577.2		c.606+677A>G		intron	N/A	NP_001186506.1
	GIMAP1-GIMAP5	NM_001303630.2		c.222+677A>G		intron	N/A	NP_001290559.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GIMAP5	ENST00000476324.1	TSL:1	n.776A>G		non_coding_transcript_exon	Exon 1 of 2
	GIMAP5	ENST00000358647.5	TSL:1 MANE Select	c.-7+677A>G		intron	N/A	ENSP00000351473.3
	GIMAP1-GIMAP5	ENST00000611999.4	TSL:5	c.606+677A>G		intron	N/A	ENSP00000477920.1

Frequencies

GnomAD3 genomes AF: 0.487 AC: 73895 AN: 151826 Hom.: 18764 Cov.: 31

Gnomad AFR AF: 0.633

Gnomad AMI AF: 0.281

Gnomad AMR AF: 0.416

Gnomad ASJ AF: 0.386

Gnomad EAS AF: 0.361

Gnomad SAS AF: 0.473

Gnomad FIN AF: 0.555

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.422

Gnomad OTH AF: 0.456

GnomAD4 exome AF: 0.371 AC: 118 AN: 318 Hom.: 25 Cov.: 0 AF XY: 0.351 AC XY: 47 AN XY: 134

African (AFR) AC: 0 AN: 0

American (AMR) AF: 0.367 AC: 11 AN: 30

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 2 AN: 4

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 0.500 AC: 1 AN: 2

European-Finnish (FIN) AF: 0.750 AC: 3 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.371 AC: 98 AN: 264

Other (OTH) AF: 0.214 AC: 3 AN: 14

GnomAD4 genome AF: 0.487 AC: 73983 AN: 151944 Hom.: 18785 Cov.: 31 AF XY: 0.492 AC XY: 36538 AN XY: 74254

African (AFR) AF: 0.633 AC: 26235 AN: 41428

American (AMR) AF: 0.417 AC: 6368 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.386 AC: 1339 AN: 3468

East Asian (EAS) AF: 0.362 AC: 1868 AN: 5162

South Asian (SAS) AF: 0.473 AC: 2278 AN: 4818

European-Finnish (FIN) AF: 0.555 AC: 5840 AN: 10528

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.422 AC: 28704 AN: 67946

Other (OTH) AF: 0.456 AC: 963 AN: 2112

Alfa AF: 0.447 Hom.: 23719

Bravo AF: 0.479

Asia WGS AF: 0.430 AC: 1495 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.87
DANN	Benign	0.57
PhyloP100		-0.64
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: rs9657891; hg19: chr7-150435473;