20-2317144-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_003245.4(TGM3):c.746G>A(p.Ser249Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.113 in 1,613,926 control chromosomes in the GnomAD database, including 11,007 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 (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_003245.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TGM3 | NM_003245.4 | c.746G>A | p.Ser249Asn | missense_variant | 6/13 | ENST00000381458.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TGM3 | ENST00000381458.6 | c.746G>A | p.Ser249Asn | missense_variant | 6/13 | 1 | NM_003245.4 | P1 | |
TGM3 | ENST00000463090.1 | n.126G>A | non_coding_transcript_exon_variant | 2/4 | 3 |
Frequencies
GnomAD3 genomes AF: 0.133 AC: 20168AN: 152046Hom.: 1490 Cov.: 31
GnomAD3 exomes AF: 0.109 AC: 27313AN: 251338Hom.: 1667 AF XY: 0.107 AC XY: 14570AN XY: 135838
GnomAD4 exome AF: 0.111 AC: 161571AN: 1461762Hom.: 9498 Cov.: 33 AF XY: 0.110 AC XY: 79685AN XY: 727174
GnomAD4 genome AF: 0.133 AC: 20219AN: 152164Hom.: 1509 Cov.: 31 AF XY: 0.130 AC XY: 9654AN XY: 74400
ClinVar
Submissions by phenotype
TGM3-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Nov 12, 2019 | 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