11-66822671-T-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6BP7
The NM_001302084.2(TOP6BL):c.1071T>A(p.Leu357Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000292 in 1,538,990 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 (no stars).
Frequency
Consequence
NM_001302084.2 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
C11orf80 | ENST00000540737.7 | c.1071T>A | p.Leu357Leu | synonymous_variant | Exon 11 of 15 | 2 | NM_001302084.2 | ENSP00000444319.1 | ||
C11orf80 | ENST00000525449.6 | c.993+907T>A | intron_variant | Intron 11 of 14 | 1 | ENSP00000434648.2 |
Frequencies
GnomAD3 genomes AF: 0.000177 AC: 27AN: 152156Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000252 AC: 4AN: 158436Hom.: 0 AF XY: 0.0000120 AC XY: 1AN XY: 83504
GnomAD4 exome AF: 0.0000130 AC: 18AN: 1386834Hom.: 0 Cov.: 28 AF XY: 0.0000131 AC XY: 9AN XY: 684642
GnomAD4 genome AF: 0.000177 AC: 27AN: 152156Hom.: 0 Cov.: 31 AF XY: 0.000175 AC XY: 13AN XY: 74344
ClinVar
Submissions by phenotype
TOP6BL-related disorder Benign:1
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