chr2-151671192-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 6P and 2B. PM2PM5PP3_ModerateBP6_Moderate
The NM_001164507.2(NEB):c.4337G>A(p.Gly1446Asp) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000496 in 1,613,900 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G1446V) has been classified as Likely pathogenic.
Frequency
Consequence
NM_001164507.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NEB | NM_001164507.2 | c.4337G>A | p.Gly1446Asp | missense_variant | 38/182 | ENST00000427231.7 | |
NEB | NM_001164508.2 | c.4337G>A | p.Gly1446Asp | missense_variant | 38/182 | ENST00000397345.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NEB | ENST00000397345.8 | c.4337G>A | p.Gly1446Asp | missense_variant | 38/182 | 5 | NM_001164508.2 | P5 | |
NEB | ENST00000427231.7 | c.4337G>A | p.Gly1446Asp | missense_variant | 38/182 | 5 | NM_001164507.2 | A2 | |
NEB | ENST00000409198.5 | c.4337G>A | p.Gly1446Asp | missense_variant | 38/150 | 5 | |||
NEB | ENST00000484968.1 | n.189G>A | non_coding_transcript_exon_variant | 1/3 | 4 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152174Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 249100Hom.: 0 AF XY: 0.00000740 AC XY: 1AN XY: 135142
GnomAD4 exome AF: 0.00000479 AC: 7AN: 1461608Hom.: 0 Cov.: 33 AF XY: 0.00000550 AC XY: 4AN XY: 727102
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152292Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74458
ClinVar
Submissions by phenotype
Nemaline myopathy 2 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 06, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at