7-150520783-G-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_153236.4(GIMAP7):c.809G>C(p.Arg270Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000106 in 1,505,746 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 Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GIMAP7 | NM_153236.4 | c.809G>C | p.Arg270Thr | missense_variant | 2/2 | ENST00000313543.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GIMAP7 | ENST00000313543.5 | c.809G>C | p.Arg270Thr | missense_variant | 2/2 | 1 | NM_153236.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000171 AC: 26AN: 151990Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000601 AC: 13AN: 216132Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 117976
GnomAD4 exome AF: 0.0000960 AC: 130AN: 1353640Hom.: 0 Cov.: 25 AF XY: 0.0000799 AC XY: 54AN XY: 676148
GnomAD4 genome ? AF: 0.000191 AC: 29AN: 152106Hom.: 0 Cov.: 32 AF XY: 0.000108 AC XY: 8AN XY: 74380
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 27, 2021 | The c.809G>C (p.R270T) alteration is located in exon 2 (coding exon 1) of the GIMAP7 gene. This alteration results from a G to C substitution at nucleotide position 809, causing the arginine (R) at amino acid position 270 to be replaced by a threonine (T). 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