rs2289292
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_004608.4(TBX6):c.1227G>C(p.Pro409=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000497 in 1,610,424 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. P409P) has been classified as Benign.
Frequency
Consequence
NM_004608.4 synonymous
Scores
Clinical Significance
Conservation
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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.1227G>C | p.Pro409= | synonymous_variant | 9/9 | ENST00000395224.7 | |
TBX6 | XM_011545926.4 | c.1227G>C | p.Pro409= | synonymous_variant | 9/9 | ||
TBX6 | XM_047434551.1 | c.1227G>C | p.Pro409= | synonymous_variant | 8/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TBX6 | ENST00000395224.7 | c.1227G>C | p.Pro409= | synonymous_variant | 9/9 | 1 | NM_004608.4 | P1 | |
TBX6 | ENST00000279386.6 | c.1227G>C | p.Pro409= | synonymous_variant | 8/8 | 1 | P1 | ||
TBX6 | ENST00000567664.5 | c.*361G>C | 3_prime_UTR_variant, NMD_transcript_variant | 7/7 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00000658 AC: 1AN: 152008Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000164 AC: 4AN: 244618Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 133162
GnomAD4 exome AF: 0.00000480 AC: 7AN: 1458298Hom.: 0 Cov.: 54 AF XY: 0.00000413 AC XY: 3AN XY: 725534
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152126Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74366
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Oct 17, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at