chr15-56093661-C-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_022841.7(RFX7):c.4067G>C(p.Gly1356Ala) variant causes a missense change. The variant allele was found at a frequency of 0.0000508 in 1,613,708 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/19 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. G1356V) has been classified as Uncertain significance.
Frequency
Consequence
NM_022841.7 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 |
---|---|---|---|---|---|---|---|
RFX7 | NM_022841.7 | c.4067G>C | p.Gly1356Ala | missense_variant | 10/10 | ENST00000559447.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RFX7 | ENST00000559447.8 | c.4067G>C | p.Gly1356Ala | missense_variant | 10/10 | 5 | NM_022841.7 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152146Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000161 AC: 4AN: 248806Hom.: 0 AF XY: 0.00000741 AC XY: 1AN XY: 134972
GnomAD4 exome AF: 0.0000547 AC: 80AN: 1461562Hom.: 0 Cov.: 32 AF XY: 0.0000550 AC XY: 40AN XY: 727058
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152146Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74324
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 17, 2022 | The c.4067G>C (p.G1356A) alteration is located in exon 9 (coding exon 9) of the RFX7 gene. This alteration results from a G to C substitution at nucleotide position 4067, causing the glycine (G) at amino acid position 1356 to be replaced by an alanine (A). 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