rs2286900
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_130759.4(GIMAP1):c.*32G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0998 in 1,475,006 control chromosomes in the GnomAD database, including 7,735 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 0.11 ( 1010 hom., cov: 32)
Exomes 𝑓: 0.099 ( 6725 hom. )
Consequence
GIMAP1
NM_130759.4 3_prime_UTR
NM_130759.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.01
Genes affected
GIMAP1 (HGNC:23237): (GTPase, IMAP family member 1) 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 is thought to be involved in the differentiation of T helper (Th) cells of the Th1 lineage, and the related mouse gene has been shown to be critical for the development of mature B and T lymphocytes. Read-through transcription exists between this gene and the downstream GIMAP5 (GTPase, IMAP family member 5) gene. [provided by RefSeq, Dec 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.187 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GIMAP1 | NM_130759.4 | c.*32G>A | 3_prime_UTR_variant | 3/3 | ENST00000307194.6 | ||
GIMAP1-GIMAP5 | NM_001199577.2 | c.402+551G>A | intron_variant | ||||
GIMAP1-GIMAP5 | NM_001303630.2 | c.18+1867G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GIMAP1 | ENST00000307194.6 | c.*32G>A | 3_prime_UTR_variant | 3/3 | 1 | NM_130759.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.109 AC: 16524AN: 152094Hom.: 1010 Cov.: 32
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GnomAD3 exomes AF: 0.109 AC: 14504AN: 133184Hom.: 794 AF XY: 0.106 AC XY: 7787AN XY: 73538
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GnomAD4 exome AF: 0.0988 AC: 130675AN: 1322794Hom.: 6725 Cov.: 28 AF XY: 0.0987 AC XY: 63901AN XY: 647636
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GnomAD4 genome ? AF: 0.109 AC: 16552AN: 152212Hom.: 1010 Cov.: 32 AF XY: 0.109 AC XY: 8149AN XY: 74438
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at