17-82050511-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_002917.2(RFNG):c.464G>A(p.Ser155Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000595 in 1,612,902 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_002917.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RFNG | NM_002917.2 | c.464G>A | p.Ser155Asn | missense_variant | 4/8 | ENST00000310496.9 | NP_002908.1 | |
RFNG | XM_011523587.3 | c.86G>A | p.Ser29Asn | missense_variant | 3/7 | XP_011521889.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RFNG | ENST00000310496.9 | c.464G>A | p.Ser155Asn | missense_variant | 4/8 | 2 | NM_002917.2 | ENSP00000307971.4 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152150Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000160 AC: 4AN: 250004Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135502
GnomAD4 exome AF: 0.0000637 AC: 93AN: 1460752Hom.: 0 Cov.: 32 AF XY: 0.0000509 AC XY: 37AN XY: 726676
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152150Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74310
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 06, 2021 | The c.464G>A (p.S155N) alteration is located in exon 4 (coding exon 4) of the RFNG gene. This alteration results from a G to A substitution at nucleotide position 464, causing the serine (S) at amino acid position 155 to be replaced by an asparagine (N). 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