2-151485796-G-C
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_001164507.2(NEB):c.25542C>G(p.Thr8514=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000685 in 1,460,556 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. T8514T) has been classified as Benign.
Frequency
Consequence
NM_001164507.2 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 |
---|---|---|---|---|---|---|---|
NEB | NM_001164507.2 | c.25542C>G | p.Thr8514= | synonymous_variant | 182/182 | ENST00000427231.7 | |
NEB | NM_001164508.2 | c.25542C>G | p.Thr8514= | synonymous_variant | 182/182 | ENST00000397345.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NEB | ENST00000397345.8 | c.25542C>G | p.Thr8514= | synonymous_variant | 182/182 | 5 | NM_001164508.2 | P5 | |
NEB | ENST00000427231.7 | c.25542C>G | p.Thr8514= | synonymous_variant | 182/182 | 5 | NM_001164507.2 | A2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000403 AC: 1AN: 248224Hom.: 0 AF XY: 0.00000743 AC XY: 1AN XY: 134546
GnomAD4 exome AF: 6.85e-7 AC: 1AN: 1460556Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 726382
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Nemaline myopathy 2 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jul 21, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at