chr7-150520620-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_153236.4(GIMAP7):c.646C>T(p.Arg216Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000374 in 1,606,276 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_153236.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GIMAP7 | NM_153236.4 | c.646C>T | p.Arg216Trp | missense_variant | 2/2 | ENST00000313543.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GIMAP7 | ENST00000313543.5 | c.646C>T | p.Arg216Trp | missense_variant | 2/2 | 1 | NM_153236.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000674 AC: 1AN: 148264Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251016Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135684
GnomAD4 exome AF: 0.00000343 AC: 5AN: 1458012Hom.: 0 Cov.: 34 AF XY: 0.00000138 AC XY: 1AN XY: 725256
GnomAD4 genome ? AF: 0.00000674 AC: 1AN: 148264Hom.: 0 Cov.: 32 AF XY: 0.0000138 AC XY: 1AN XY: 72360
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 03, 2024 | The c.646C>T (p.R216W) alteration is located in exon 2 (coding exon 1) of the GIMAP7 gene. This alteration results from a C to T substitution at nucleotide position 646, causing the arginine (R) at amino acid position 216 to be replaced by a tryptophan (W). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at