rs115379999
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_ModerateBP6_Very_StrongBP7BS1BS2_Supporting
The NM_001164507.2(NEB):c.5718C>T(p.Ala1906=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000316 in 1,613,088 control chromosomes in the GnomAD database, including 4 homozygotes. 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. A1906A) has been classified as Likely benign.
Frequency
Consequence
NM_001164507.2 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NEB | NM_001164507.2 | c.5718C>T | p.Ala1906= | synonymous_variant | 45/182 | ENST00000427231.7 | |
NEB | NM_001164508.2 | c.5718C>T | p.Ala1906= | synonymous_variant | 45/182 | ENST00000397345.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NEB | ENST00000397345.8 | c.5718C>T | p.Ala1906= | synonymous_variant | 45/182 | 5 | NM_001164508.2 | P5 | |
NEB | ENST00000427231.7 | c.5718C>T | p.Ala1906= | synonymous_variant | 45/182 | 5 | NM_001164507.2 | A2 | |
NEB | ENST00000409198.5 | c.5718C>T | p.Ala1906= | synonymous_variant | 45/150 | 5 |
Frequencies
GnomAD3 genomes AF: 0.00151 AC: 230AN: 152166Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000374 AC: 93AN: 248336Hom.: 0 AF XY: 0.000252 AC XY: 34AN XY: 134730
GnomAD4 exome AF: 0.000191 AC: 279AN: 1460804Hom.: 3 Cov.: 31 AF XY: 0.000160 AC XY: 116AN XY: 726552
GnomAD4 genome AF: 0.00152 AC: 231AN: 152284Hom.: 1 Cov.: 32 AF XY: 0.00152 AC XY: 113AN XY: 74454
ClinVar
Submissions by phenotype
not specified Benign:2
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 27, 2017 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Nemaline myopathy 2 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at