7-150738355-C-T

Variant names:

• chr7-150738355-C-T
• rs9657890
• ENST00000476324.1:n.746C>T

Variant summary

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

The ENST00000476324.1(GIMAP5):​n.746C>T 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 0.376 in 152,480 control chromosomes in the GnomAD database, including 11,761 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 0.38 (11736 hom., cov: 31)
  • Exomes 𝑓: 0.31 (25 hom.)
• Consequence: GIMAP5 ENST00000476324.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08
• Publications: 4 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 = 0.534 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+647C>T		intron	N/A	NP_060854.2
	GIMAP1-GIMAP5	NM_001199577.2		c.606+647C>T		intron	N/A	NP_001186506.1
	GIMAP1-GIMAP5	NM_001303630.2		c.222+647C>T		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.746C>T		non_coding_transcript_exon	Exon 1 of 2
	GIMAP5	ENST00000358647.5	TSL:1 MANE Select	c.-7+647C>T		intron	N/A	ENSP00000351473.3
	GIMAP1-GIMAP5	ENST00000611999.4	TSL:5	c.606+647C>T		intron	N/A	ENSP00000477920.1

Frequencies

GnomAD3 genomes AF: 0.376 AC: 57139 AN: 151788 Hom.: 11719 Cov.: 31

Gnomad AFR AF: 0.540

Gnomad AMI AF: 0.164

Gnomad AMR AF: 0.282

Gnomad ASJ AF: 0.336

Gnomad EAS AF: 0.273

Gnomad SAS AF: 0.375

Gnomad FIN AF: 0.401

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.308

Gnomad OTH AF: 0.346

GnomAD4 exome AF: 0.314 AC: 180 AN: 574 Hom.: 25 Cov.: 0 AF XY: 0.343 AC XY: 96 AN XY: 280

African (AFR) AF: 0.500 AC: 1 AN: 2

American (AMR) AF: 0.289 AC: 22 AN: 76

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

East Asian (EAS) AF: 0.00 AC: 0 AN: 2

South Asian (SAS) AF: 0.250 AC: 1 AN: 4

European-Finnish (FIN) AF: 0.250 AC: 1 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.314 AC: 145 AN: 462

Other (OTH) AF: 0.400 AC: 8 AN: 20

GnomAD4 genome AF: 0.377 AC: 57205 AN: 151906 Hom.: 11736 Cov.: 31 AF XY: 0.379 AC XY: 28110 AN XY: 74208

African (AFR) AF: 0.540 AC: 22354 AN: 41384

American (AMR) AF: 0.281 AC: 4300 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.336 AC: 1167 AN: 3470

East Asian (EAS) AF: 0.273 AC: 1406 AN: 5150

South Asian (SAS) AF: 0.375 AC: 1806 AN: 4820

European-Finnish (FIN) AF: 0.401 AC: 4221 AN: 10528

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.308 AC: 20961 AN: 67962

Other (OTH) AF: 0.348 AC: 734 AN: 2112

Alfa AF: 0.231 Hom.: 558

Bravo AF: 0.372

Asia WGS AF: 0.331 AC: 1154 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	4.1
DANN	Benign	0.49
PhyloP100		-1.1
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: rs9657890; hg19: chr7-150435443;