chr2-151636274-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP6
The NM_001164508.2(NEB):c.9055G>A(p.Ala3019Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000789 in 1,609,944 control chromosomes in the GnomAD database, including 1 homozygotes. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A3019V) has been classified as Uncertain significance.
Frequency
Consequence
NM_001164508.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NEB | ENST00000397345.8 | c.9055G>A | p.Ala3019Thr | missense_variant | Exon 64 of 182 | 5 | NM_001164508.2 | ENSP00000380505.3 | ||
NEB | ENST00000427231.7 | c.9055G>A | p.Ala3019Thr | missense_variant | Exon 64 of 182 | 5 | NM_001164507.2 | ENSP00000416578.2 | ||
NEB | ENST00000409198.5 | c.8853+3619G>A | intron_variant | Intron 62 of 149 | 5 | ENSP00000386259.1 |
Frequencies
GnomAD3 genomes AF: 0.0000591 AC: 9AN: 152196Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000528 AC: 13AN: 246190Hom.: 0 AF XY: 0.0000673 AC XY: 9AN XY: 133828
GnomAD4 exome AF: 0.0000809 AC: 118AN: 1457748Hom.: 1 Cov.: 31 AF XY: 0.0000772 AC XY: 56AN XY: 725274
GnomAD4 genome AF: 0.0000591 AC: 9AN: 152196Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74344
ClinVar
Submissions by phenotype
Nemaline myopathy 2 Uncertain:1Benign:1
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not provided Uncertain:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at