16-30086258-G-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_004608.4(TBX6):c.1278C>A(p.Gly426=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000136 in 1,612,122 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. G426G) has been classified as Uncertain significance.
Frequency
Consequence
NM_004608.4 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TBX6 | NM_004608.4 | c.1278C>A | p.Gly426= | synonymous_variant | 9/9 | ENST00000395224.7 | |
TBX6 | XM_011545926.4 | c.1278C>A | p.Gly426= | synonymous_variant | 9/9 | ||
TBX6 | XM_047434551.1 | c.1278C>A | p.Gly426= | synonymous_variant | 8/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TBX6 | ENST00000395224.7 | c.1278C>A | p.Gly426= | synonymous_variant | 9/9 | 1 | NM_004608.4 | P1 | |
TBX6 | ENST00000279386.6 | c.1278C>A | p.Gly426= | synonymous_variant | 8/8 | 1 | P1 | ||
TBX6 | ENST00000567664.5 | c.*412C>A | 3_prime_UTR_variant, NMD_transcript_variant | 7/7 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152156Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000321 AC: 8AN: 248846Hom.: 0 AF XY: 0.0000445 AC XY: 6AN XY: 134794
GnomAD4 exome AF: 0.0000123 AC: 18AN: 1459848Hom.: 0 Cov.: 31 AF XY: 0.0000165 AC XY: 12AN XY: 726258
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152274Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74476
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | May 05, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at