rs35555631
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001164508.2(NEB):c.8072G>A(p.Arg2691His) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000314 in 1,613,840 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001164508.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NEB | ENST00000397345.8 | c.8072G>A | p.Arg2691His | missense_variant | Exon 58 of 182 | 5 | NM_001164508.2 | ENSP00000380505.3 | ||
NEB | ENST00000427231.7 | c.8072G>A | p.Arg2691His | missense_variant | Exon 58 of 182 | 5 | NM_001164507.2 | ENSP00000416578.2 | ||
NEB | ENST00000409198.5 | c.8072G>A | p.Arg2691His | missense_variant | Exon 58 of 150 | 5 | ENSP00000386259.1 |
Frequencies
GnomAD3 genomes AF: 0.00149 AC: 227AN: 152110Hom.: 2 Cov.: 33
GnomAD3 exomes AF: 0.000377 AC: 94AN: 249120Hom.: 0 AF XY: 0.000289 AC XY: 39AN XY: 135138
GnomAD4 exome AF: 0.000190 AC: 277AN: 1461612Hom.: 4 Cov.: 31 AF XY: 0.000190 AC XY: 138AN XY: 727094
GnomAD4 genome AF: 0.00150 AC: 229AN: 152228Hom.: 2 Cov.: 33 AF XY: 0.00138 AC XY: 103AN XY: 74450
ClinVar
Submissions by phenotype
not specified Benign:2
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p.Arg2691His in exon 58 of NEB: This variant is not expected to have clinical si gnificance because it has been identified in 0.6% (55/9800) of African chromosom es by the Exome Aggregation Consortium (ExAC, http://exac.broadinstitute.org; db SNP rs35555631). -
NEB-related disorder Benign:1
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). -
not provided Benign:1
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Nemaline myopathy 2 Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at