15-56093977-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_022841.7(RFX7):c.3751A>G(p.Asn1251Asp) variant causes a missense change. The variant allele was found at a frequency of 0.00000806 in 1,613,814 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. N1251S) has been classified as Likely benign.
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.3751A>G | p.Asn1251Asp | missense_variant | 10/10 | ENST00000559447.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RFX7 | ENST00000559447.8 | c.3751A>G | p.Asn1251Asp | missense_variant | 10/10 | 5 | NM_022841.7 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152144Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000803 AC: 2AN: 248916Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135026
GnomAD4 exome AF: 0.00000753 AC: 11AN: 1461670Hom.: 0 Cov.: 33 AF XY: 0.00000825 AC XY: 6AN XY: 727124
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152144Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74312
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 11, 2023 | The c.3751A>G (p.N1251D) alteration is located in exon 9 (coding exon 9) of the RFX7 gene. This alteration results from a A to G substitution at nucleotide position 3751, causing the asparagine (N) at amino acid position 1251 to be replaced by an aspartic acid (D). 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