chr6-13305116-C-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_016495.6(TBC1D7):c.867G>T(p.Pro289=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000874 in 1,612,686 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. P289P) has been classified as Likely benign.
Frequency
Consequence
NM_016495.6 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 |
---|---|---|---|---|---|---|---|
TBC1D7 | NM_016495.6 | c.867G>T | p.Pro289= | synonymous_variant | 8/8 | ENST00000379300.8 | |
TBC1D7-LOC100130357 | NR_134872.2 | n.610-10218G>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TBC1D7 | ENST00000379300.8 | c.867G>T | p.Pro289= | synonymous_variant | 8/8 | 1 | NM_016495.6 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000394 AC: 60AN: 152166Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000112 AC: 28AN: 249238Hom.: 0 AF XY: 0.0000668 AC XY: 9AN XY: 134650
GnomAD4 exome AF: 0.0000555 AC: 81AN: 1460402Hom.: 0 Cov.: 30 AF XY: 0.0000482 AC XY: 35AN XY: 726508
GnomAD4 genome AF: 0.000394 AC: 60AN: 152284Hom.: 0 Cov.: 33 AF XY: 0.000416 AC XY: 31AN XY: 74460
ClinVar
Submissions by phenotype
TBC1D7-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Sep 17, 2019 | This variant is classified as likely 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