rs778982089
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2BP4_ModerateBP6
The NM_001164507.2(NEB):c.17900C>T(p.Thr5967Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000849 in 1,613,372 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. T5967T) has been classified as Likely benign.
Frequency
Consequence
NM_001164507.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NEB | NM_001164507.2 | c.17900C>T | p.Thr5967Met | missense_variant | 114/182 | ENST00000427231.7 | |
NEB | NM_001164508.2 | c.17900C>T | p.Thr5967Met | missense_variant | 114/182 | ENST00000397345.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NEB | ENST00000397345.8 | c.17900C>T | p.Thr5967Met | missense_variant | 114/182 | 5 | NM_001164508.2 | P5 | |
NEB | ENST00000427231.7 | c.17900C>T | p.Thr5967Met | missense_variant | 114/182 | 5 | NM_001164507.2 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000460 AC: 7AN: 152060Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000604 AC: 15AN: 248290Hom.: 0 AF XY: 0.0000520 AC XY: 7AN XY: 134670
GnomAD4 exome AF: 0.0000890 AC: 130AN: 1461312Hom.: 0 Cov.: 31 AF XY: 0.0000853 AC XY: 62AN XY: 726898
GnomAD4 genome ? AF: 0.0000460 AC: 7AN: 152060Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74258
ClinVar
Submissions by phenotype
Nemaline myopathy 2 Uncertain:1Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 24, 2024 | - - |
Uncertain significance, no assertion criteria provided | clinical testing | Natera, Inc. | Aug 19, 2020 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at