6-166929662-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_003730.6(RNASET2):c.697G>A(p.Ala233Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000978 in 1,614,092 control chromosomes in the GnomAD database, including 14 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Synonymous variant affecting the same amino acid position (i.e. A233A) has been classified as Likely benign.
Frequency
Consequence
NM_003730.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RNASET2 | ENST00000508775.6 | c.697G>A | p.Ala233Thr | missense_variant | Exon 9 of 9 | 1 | NM_003730.6 | ENSP00000426455.2 | ||
ENSG00000249141 | ENST00000507747.1 | c.432+4429G>A | intron_variant | Intron 7 of 7 | 5 | ENSP00000426906.1 |
Frequencies
GnomAD3 genomes AF: 0.00556 AC: 846AN: 152126Hom.: 9 Cov.: 33
GnomAD3 exomes AF: 0.00140 AC: 352AN: 251396Hom.: 3 AF XY: 0.000979 AC XY: 133AN XY: 135898
GnomAD4 exome AF: 0.000498 AC: 728AN: 1461848Hom.: 5 Cov.: 31 AF XY: 0.000396 AC XY: 288AN XY: 727220
GnomAD4 genome AF: 0.00558 AC: 850AN: 152244Hom.: 9 Cov.: 33 AF XY: 0.00541 AC XY: 403AN XY: 74436
ClinVar
Submissions by phenotype
not provided Benign:1
- -
RNASET2-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at