2-151666141-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.4980C>G(p.Pro1660=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000124 in 1,613,724 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. P1660P) has been classified as Likely 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.4980C>G | p.Pro1660= | synonymous_variant | 41/182 | ENST00000427231.7 | |
NEB | NM_001164508.2 | c.4980C>G | p.Pro1660= | synonymous_variant | 41/182 | ENST00000397345.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NEB | ENST00000397345.8 | c.4980C>G | p.Pro1660= | synonymous_variant | 41/182 | 5 | NM_001164508.2 | P5 | |
NEB | ENST00000427231.7 | c.4980C>G | p.Pro1660= | synonymous_variant | 41/182 | 5 | NM_001164507.2 | A2 | |
NEB | ENST00000409198.5 | c.4980C>G | p.Pro1660= | synonymous_variant | 41/150 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152128Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 248968Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135058
GnomAD4 exome AF: 0.0000130 AC: 19AN: 1461596Hom.: 0 Cov.: 31 AF XY: 0.0000124 AC XY: 9AN XY: 727074
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152128Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74322
ClinVar
Submissions by phenotype
Nemaline myopathy 2 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 26, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at