rs9657879

Variant names:

• chr7-150739109-T-C
• rs9657879
• ENST00000476324.1:n.1500T>C

Variant summary

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

The ENST00000476324.1(GIMAP5):​n.1500T>C 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 0.179 in 152,220 control chromosomes in the GnomAD database, including 2,688 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 0.18 (2688 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: GIMAP5 ENST00000476324.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.313
• Publications: 2 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=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.249 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GIMAP5	NM_018384.5	c.-7+1401T>C		intron_variant	Intron 1 of 2	ENST00000358647.5	NP_060854.2
GIMAP1-GIMAP5	NM_001199577.2	c.606+1401T>C		intron_variant	Intron 4 of 5		NP_001186506.1
GIMAP1-GIMAP5	NM_001303630.2	c.222+1401T>C		intron_variant	Intron 3 of 4		NP_001290559.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GIMAP5	ENST00000358647.5	c.-7+1401T>C		intron_variant	Intron 1 of 2	1	NM_018384.5	ENSP00000351473.3
GIMAP1-GIMAP5	ENST00000611999.4	c.606+1401T>C		intron_variant	Intron 4 of 5	5		ENSP00000477920.1

Frequencies

GnomAD3 genomes AF: 0.179 AC: 27219 AN: 152102 Hom.: 2687 Cov.: 32

Gnomad AFR AF: 0.253

Gnomad AMI AF: 0.0736

Gnomad AMR AF: 0.141

Gnomad ASJ AF: 0.191

Gnomad EAS AF: 0.0112

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.125

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.174

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.179 AC: 27235 AN: 152220 Hom.: 2688 Cov.: 32 AF XY: 0.174 AC XY: 12989 AN XY: 74440

African (AFR) AF: 0.253 AC: 10509 AN: 41528

American (AMR) AF: 0.141 AC: 2151 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.191 AC: 662 AN: 3468

East Asian (EAS) AF: 0.0112 AC: 58 AN: 5188

South Asian (SAS) AF: 0.110 AC: 530 AN: 4828

European-Finnish (FIN) AF: 0.125 AC: 1325 AN: 10602

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.169 AC: 11491 AN: 67992

Other (OTH) AF: 0.176 AC: 372 AN: 2114

Alfa AF: 0.205 Hom.: 959

Bravo AF: 0.182

Asia WGS AF: 0.0690 AC: 242 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.5
DANN	Benign	0.74
PhyloP100		-0.31
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: rs9657879; hg19: chr7-150436197;