rs769233880
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2BP4_ModerateBP6
The NM_001164507.2(NEB):c.3203C>T(p.Thr1068Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000938 in 1,609,168 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 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. T1068T) 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.3203C>T | p.Thr1068Ile | missense_variant | 32/182 | ENST00000427231.7 | |
NEB | NM_001164508.2 | c.3203C>T | p.Thr1068Ile | missense_variant | 32/182 | ENST00000397345.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NEB | ENST00000397345.8 | c.3203C>T | p.Thr1068Ile | missense_variant | 32/182 | 5 | NM_001164508.2 | P5 | |
NEB | ENST00000427231.7 | c.3203C>T | p.Thr1068Ile | missense_variant | 32/182 | 5 | NM_001164507.2 | A2 | |
NEB | ENST00000409198.5 | c.3203C>T | p.Thr1068Ile | missense_variant | 32/150 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000198 AC: 3AN: 151374Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000401 AC: 10AN: 249220Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 135208
GnomAD4 exome AF: 0.000102 AC: 148AN: 1457794Hom.: 0 Cov.: 33 AF XY: 0.0000993 AC XY: 72AN XY: 725254
GnomAD4 genome AF: 0.0000198 AC: 3AN: 151374Hom.: 0 Cov.: 31 AF XY: 0.0000271 AC XY: 2AN XY: 73898
ClinVar
Submissions by phenotype
Nemaline myopathy 2 Uncertain:1Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 19, 2023 | - - |
Uncertain significance, no assertion criteria provided | clinical testing | Natera, Inc. | Nov 11, 2019 | - - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Mar 17, 2020 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at