rs183354017
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001164508.2(NEB):āc.8024A>Gā(p.Asp2675Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000158 in 1,613,898 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001164508.2 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NEB | NM_001164507.2 | c.8024A>G | p.Asp2675Gly | missense_variant | 58/182 | ENST00000427231.7 | NP_001157979.2 | |
NEB | NM_001164508.2 | c.8024A>G | p.Asp2675Gly | missense_variant | 58/182 | ENST00000397345.8 | NP_001157980.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NEB | ENST00000397345.8 | c.8024A>G | p.Asp2675Gly | missense_variant | 58/182 | 5 | NM_001164508.2 | ENSP00000380505 | P5 | |
NEB | ENST00000427231.7 | c.8024A>G | p.Asp2675Gly | missense_variant | 58/182 | 5 | NM_001164507.2 | ENSP00000416578 | A2 | |
NEB | ENST00000409198.5 | c.8024A>G | p.Asp2675Gly | missense_variant | 58/150 | 5 | ENSP00000386259 |
Frequencies
GnomAD3 genomes AF: 0.000256 AC: 39AN: 152140Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000108 AC: 27AN: 249056Hom.: 0 AF XY: 0.0000962 AC XY: 13AN XY: 135104
GnomAD4 exome AF: 0.000148 AC: 216AN: 1461640Hom.: 1 Cov.: 31 AF XY: 0.000129 AC XY: 94AN XY: 727106
GnomAD4 genome AF: 0.000256 AC: 39AN: 152258Hom.: 0 Cov.: 33 AF XY: 0.000255 AC XY: 19AN XY: 74450
ClinVar
Submissions by phenotype
Nemaline myopathy 2 Uncertain:2Benign:1
Uncertain significance, criteria provided, single submitter | clinical testing | Baylor Genetics | Dec 17, 2019 | This variant was determined to be of uncertain significance according to ACMG Guidelines, 2015 [PMID:25741868]. - |
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 29, 2024 | - - |
Uncertain significance, no assertion criteria provided | clinical testing | Natera, Inc. | Nov 11, 2019 | - - |
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 30, 2024 | The c.8024A>G (p.D2675G) alteration is located in exon 58 (coding exon 56) of the NEB gene. This alteration results from a A to G substitution at nucleotide position 8024, causing the aspartic acid (D) at amino acid position 2675 to be replaced by a glycine (G). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Jun 07, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at