2-151680785-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 4P and 2B. PM2PP3_ModerateBP6_Moderate
The NM_001164507.2(NEB):āc.2987T>Cā(p.Ile996Thr) variant causes a missense change. The variant allele was found at a frequency of 0.000013 in 1,461,244 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. I996N) has been classified as Likely benign.
Frequency
Consequence
NM_001164507.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NEB | NM_001164507.2 | c.2987T>C | p.Ile996Thr | missense_variant | 30/182 | ENST00000427231.7 | |
NEB | NM_001164508.2 | c.2987T>C | p.Ile996Thr | missense_variant | 30/182 | ENST00000397345.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NEB | ENST00000397345.8 | c.2987T>C | p.Ile996Thr | missense_variant | 30/182 | 5 | NM_001164508.2 | P5 | |
NEB | ENST00000427231.7 | c.2987T>C | p.Ile996Thr | missense_variant | 30/182 | 5 | NM_001164507.2 | A2 | |
NEB | ENST00000409198.5 | c.2987T>C | p.Ile996Thr | missense_variant | 30/150 | 5 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000803 AC: 2AN: 249188Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135186
GnomAD4 exome AF: 0.0000130 AC: 19AN: 1461244Hom.: 0 Cov.: 30 AF XY: 0.0000138 AC XY: 10AN XY: 726924
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Nemaline myopathy 2 Uncertain:1Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jul 06, 2022 | - - |
Uncertain significance, no assertion criteria provided | clinical testing | Natera, Inc. | Nov 11, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at