chrX-153504652-C-T
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_001711.6(BGN):c.21C>T(p.Leu7=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000133 in 1,206,566 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 4 hemizygotes in GnomAD. 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. L7L) has been classified as Uncertain significance.
Frequency
Consequence
NM_001711.6 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -15 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BGN | NM_001711.6 | c.21C>T | p.Leu7= | synonymous_variant | 2/8 | ENST00000331595.9 | |
BGN | XM_017029724.3 | c.21C>T | p.Leu7= | synonymous_variant | 1/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BGN | ENST00000331595.9 | c.21C>T | p.Leu7= | synonymous_variant | 2/8 | 1 | NM_001711.6 | P1 | |
BGN | ENST00000431891.1 | c.21C>T | p.Leu7= | synonymous_variant | 2/5 | 5 | |||
BGN | ENST00000472615.5 | n.165C>T | non_coding_transcript_exon_variant | 2/8 | 5 | ||||
BGN | ENST00000480756.1 | n.163C>T | non_coding_transcript_exon_variant | 2/8 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000266 AC: 3AN: 112835Hom.: 0 Cov.: 25 AF XY: 0.0000286 AC XY: 1AN XY: 34981
GnomAD3 exomes AF: 0.0000444 AC: 8AN: 180299Hom.: 0 AF XY: 0.0000307 AC XY: 2AN XY: 65141
GnomAD4 exome AF: 0.0000119 AC: 13AN: 1093731Hom.: 0 Cov.: 30 AF XY: 0.00000834 AC XY: 3AN XY: 359785
GnomAD4 genome ? AF: 0.0000266 AC: 3AN: 112835Hom.: 0 Cov.: 25 AF XY: 0.0000286 AC XY: 1AN XY: 34981
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Oct 04, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at