rs114959904
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BS1BS2
The NM_001164508.2(NEB):c.2640C>T(p.Arg880Arg) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000793 in 1,596,906 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001164508.2 splice_region, synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NEB | NM_001164507.2 | c.2640C>T | p.Arg880Arg | splice_region_variant, synonymous_variant | 28/182 | ENST00000427231.7 | NP_001157979.2 | |
NEB | NM_001164508.2 | c.2640C>T | p.Arg880Arg | splice_region_variant, synonymous_variant | 28/182 | ENST00000397345.8 | NP_001157980.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NEB | ENST00000397345.8 | c.2640C>T | p.Arg880Arg | splice_region_variant, synonymous_variant | 28/182 | 5 | NM_001164508.2 | ENSP00000380505.3 | ||
NEB | ENST00000427231.7 | c.2640C>T | p.Arg880Arg | splice_region_variant, synonymous_variant | 28/182 | 5 | NM_001164507.2 | ENSP00000416578.2 | ||
NEB | ENST00000409198.5 | c.2640C>T | p.Arg880Arg | splice_region_variant, synonymous_variant | 28/150 | 5 | ENSP00000386259.1 |
Frequencies
GnomAD3 genomes AF: 0.00403 AC: 613AN: 152112Hom.: 4 Cov.: 32
GnomAD3 exomes AF: 0.000927 AC: 207AN: 223304Hom.: 2 AF XY: 0.000833 AC XY: 100AN XY: 120096
GnomAD4 exome AF: 0.000453 AC: 654AN: 1444676Hom.: 3 Cov.: 30 AF XY: 0.000367 AC XY: 263AN XY: 717024
GnomAD4 genome AF: 0.00402 AC: 612AN: 152230Hom.: 4 Cov.: 32 AF XY: 0.00386 AC XY: 287AN XY: 74442
ClinVar
Submissions by phenotype
not provided Benign:3
Benign, criteria provided, single submitter | clinical testing | GeneDx | Aug 22, 2018 | - - |
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Jun 11, 2018 | - - |
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jun 01, 2024 | NEB: BP4, BP7, BS1, BS2 - |
Nemaline myopathy 2 Benign:2
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 27, 2024 | - - |
Benign, no assertion criteria provided | clinical testing | Natera, Inc. | Dec 05, 2019 | - - |
not specified Benign:1
Likely benign, no assertion criteria provided | clinical testing | Genetic Services Laboratory, University of Chicago | - | Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at