rs143473183
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 2P and 9B. PM2BP4_StrongBP6BS1
The NM_001164508.2(NEB):c.9181A>T(p.Met3061Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00027 in 1,613,996 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/17 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 Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NEB | NM_001164507.2 | c.9181A>T | p.Met3061Leu | missense_variant | 65/182 | ENST00000427231.7 | NP_001157979.2 | |
NEB | NM_001164508.2 | c.9181A>T | p.Met3061Leu | missense_variant | 65/182 | ENST00000397345.8 | NP_001157980.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NEB | ENST00000397345.8 | c.9181A>T | p.Met3061Leu | missense_variant | 65/182 | 5 | NM_001164508.2 | ENSP00000380505 | P5 | |
NEB | ENST00000427231.7 | c.9181A>T | p.Met3061Leu | missense_variant | 65/182 | 5 | NM_001164507.2 | ENSP00000416578 | A2 | |
NEB | ENST00000409198.5 | c.8854-2709A>T | intron_variant | 5 | ENSP00000386259 |
Frequencies
GnomAD3 genomes AF: 0.00143 AC: 217AN: 152174Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000341 AC: 85AN: 249256Hom.: 0 AF XY: 0.000266 AC XY: 36AN XY: 135218
GnomAD4 exome AF: 0.000143 AC: 209AN: 1461704Hom.: 0 Cov.: 115 AF XY: 0.000132 AC XY: 96AN XY: 727134
GnomAD4 genome AF: 0.00149 AC: 227AN: 152292Hom.: 1 Cov.: 32 AF XY: 0.00162 AC XY: 121AN XY: 74474
ClinVar
Submissions by phenotype
not provided Uncertain:2Benign:1
Uncertain significance, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Aug 07, 2019 | - - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | May 21, 2018 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Athena Diagnostics | Jul 20, 2018 | - - |
Nemaline myopathy 2 Uncertain:1Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 24, 2024 | - - |
Uncertain significance, no assertion criteria provided | clinical testing | Natera, Inc. | Jan 17, 2020 | - - |
NEB-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Jun 08, 2020 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at