chr8-13012774-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6_Moderate
The NM_020844.3(TRMT9B):c.245A>G(p.Asn82Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000101 in 1,613,854 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 Likely benign (★).
Frequency
Consequence
NM_020844.3 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 |
---|---|---|---|---|---|---|---|
TRMT9B | NM_020844.3 | c.245A>G | p.Asn82Ser | missense_variant | 4/5 | ENST00000524591.7 | |
LOC124901889 | XR_007060825.1 | n.491+1566T>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRMT9B | ENST00000524591.7 | c.245A>G | p.Asn82Ser | missense_variant | 4/5 | 5 | NM_020844.3 | P1 | |
TRMT9B | ENST00000529978.1 | n.762A>G | non_coding_transcript_exon_variant | 1/2 | 1 | ||||
TRMT9B | ENST00000447063.6 | c.245A>G | p.Asn82Ser | missense_variant | 5/6 | 2 | |||
TRMT9B | ENST00000529706.1 | n.2513A>G | non_coding_transcript_exon_variant | 1/2 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000394 AC: 6AN: 152152Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000562 AC: 14AN: 249118Hom.: 0 AF XY: 0.0000666 AC XY: 9AN XY: 135174
GnomAD4 exome AF: 0.000107 AC: 157AN: 1461702Hom.: 0 Cov.: 32 AF XY: 0.0000990 AC XY: 72AN XY: 727130
GnomAD4 genome ? AF: 0.0000394 AC: 6AN: 152152Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74328
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | May 18, 2022 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at