chr17-82050518-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.457G>A(p.Ala153Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000136 in 1,612,708 control chromosomes in the GnomAD database, including 1 homozygotes. 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. A153S) has been classified 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 | UniProt |
---|---|---|---|---|---|---|---|
RFNG | NM_002917.2 | c.457G>A | p.Ala153Thr | missense_variant | 4/8 | ENST00000310496.9 | |
RFNG | XM_011523587.3 | c.79G>A | p.Ala27Thr | missense_variant | 3/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RFNG | ENST00000310496.9 | c.457G>A | p.Ala153Thr | missense_variant | 4/8 | 2 | NM_002917.2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152152Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000280 AC: 7AN: 249780Hom.: 0 AF XY: 0.00000739 AC XY: 1AN XY: 135408
GnomAD4 exome AF: 0.0000116 AC: 17AN: 1460556Hom.: 1 Cov.: 36 AF XY: 0.0000110 AC XY: 8AN XY: 726578
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152152Hom.: 0 Cov.: 34 AF XY: 0.0000404 AC XY: 3AN XY: 74332
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 19, 2022 | The c.457G>A (p.A153T) 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 457, causing the alanine (A) at amino acid position 153 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