2-151709676-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6_Moderate
The NM_001164507.2(NEB):c.1015G>A(p.Ala339Thr) variant causes a missense change. The variant allele was found at a frequency of 0.00000553 in 1,446,636 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A339V) has been classified as Uncertain significance.
Frequency
Consequence
NM_001164507.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NEB | NM_001164507.2 | c.1015G>A | p.Ala339Thr | missense_variant | 12/182 | ENST00000427231.7 | |
NEB | NM_001164508.2 | c.1015G>A | p.Ala339Thr | missense_variant | 12/182 | ENST00000397345.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NEB | ENST00000397345.8 | c.1015G>A | p.Ala339Thr | missense_variant | 12/182 | 5 | NM_001164508.2 | P5 | |
NEB | ENST00000427231.7 | c.1015G>A | p.Ala339Thr | missense_variant | 12/182 | 5 | NM_001164507.2 | A2 | |
NEB | ENST00000409198.5 | c.1015G>A | p.Ala339Thr | missense_variant | 12/150 | 5 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000439 AC: 10AN: 227558Hom.: 0 AF XY: 0.0000489 AC XY: 6AN XY: 122590
GnomAD4 exome AF: 0.00000553 AC: 8AN: 1446636Hom.: 0 Cov.: 30 AF XY: 0.00000696 AC XY: 5AN XY: 718018
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Nemaline myopathy 2 Uncertain:1Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 04, 2024 | - - |
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