chr2-151553405-C-T
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2BP4_ModerateBP6
The NM_001164507.2(NEB):c.19724G>A(p.Arg6575His) variant causes a missense change. The variant allele was found at a frequency of 0.000036 in 1,610,522 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 Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R6575C) 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 -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NEB | NM_001164507.2 | c.19724G>A | p.Arg6575His | missense_variant | 127/182 | ENST00000427231.7 | |
NEB | NM_001164508.2 | c.19724G>A | p.Arg6575His | missense_variant | 127/182 | ENST00000397345.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NEB | ENST00000397345.8 | c.19724G>A | p.Arg6575His | missense_variant | 127/182 | 5 | NM_001164508.2 | P5 | |
NEB | ENST00000427231.7 | c.19724G>A | p.Arg6575His | missense_variant | 127/182 | 5 | NM_001164507.2 | A2 |
Frequencies
GnomAD3 genomes AF: 0.0000789 AC: 12AN: 152112Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000322 AC: 8AN: 248726Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 134904
GnomAD4 exome AF: 0.0000315 AC: 46AN: 1458292Hom.: 0 Cov.: 30 AF XY: 0.0000303 AC XY: 22AN XY: 725754
GnomAD4 genome AF: 0.0000788 AC: 12AN: 152230Hom.: 0 Cov.: 32 AF XY: 0.0000537 AC XY: 4AN XY: 74420
ClinVar
Submissions by phenotype
Nemaline myopathy 2 Uncertain:1Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 02, 2023 | - - |
Uncertain significance, no assertion criteria provided | clinical testing | Natera, Inc. | Jan 17, 2020 | - - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Aug 29, 2022 | - - |
Nemaline myopathy 2;C5543431:Arthrogryposis multiplex congenita 6 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Jul 15, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at