3-141807786-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_139209.3(GRK7):c.1192G>A(p.Val398Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000031 in 1,614,196 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V398F) has been classified as Uncertain significance.
Frequency
Consequence
NM_139209.3 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 |
---|---|---|---|---|---|---|---|
GRK7 | NM_139209.3 | c.1192G>A | p.Val398Ile | missense_variant | 5/6 | ENST00000682958.1 | |
GRK7 | XM_047447449.1 | c.1192G>A | p.Val398Ile | missense_variant | 6/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GRK7 | ENST00000682958.1 | c.1192G>A | p.Val398Ile | missense_variant | 5/6 | NM_139209.3 | P1 | ||
GRK7 | ENST00000264952.2 | c.1192G>A | p.Val398Ile | missense_variant | 3/4 | 1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152204Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000318 AC: 8AN: 251404Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135856
GnomAD4 exome AF: 0.0000335 AC: 49AN: 1461874Hom.: 0 Cov.: 31 AF XY: 0.0000303 AC XY: 22AN XY: 727242
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152322Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74494
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 23, 2023 | The c.1192G>A (p.V398I) alteration is located in exon 3 (coding exon 3) of the GRK7 gene. This alteration results from a G to A substitution at nucleotide position 1192, causing the valine (V) at amino acid position 398 to be replaced by an isoleucine (I). 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