rs775531807
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PM4
The NM_001164507.2(NEB):โc.5698_5703delโ(p.Tyr1900_Asn1901del) variant causes a inframe deletion change. The variant allele was found at a frequency of 0.000353 in 1,613,446 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. Y1900Y) has been classified as Likely benign.
Frequency
Consequence
NM_001164507.2 inframe_deletion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NEB | NM_001164507.2 | c.5698_5703del | p.Tyr1900_Asn1901del | inframe_deletion | 45/182 | ENST00000427231.7 | |
NEB | NM_001164508.2 | c.5698_5703del | p.Tyr1900_Asn1901del | inframe_deletion | 45/182 | ENST00000397345.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NEB | ENST00000397345.8 | c.5698_5703del | p.Tyr1900_Asn1901del | inframe_deletion | 45/182 | 5 | NM_001164508.2 | P5 | |
NEB | ENST00000427231.7 | c.5698_5703del | p.Tyr1900_Asn1901del | inframe_deletion | 45/182 | 5 | NM_001164507.2 | A2 | |
NEB | ENST00000409198.5 | c.5698_5703del | p.Tyr1900_Asn1901del | inframe_deletion | 45/150 | 5 |
Frequencies
GnomAD3 genomes AF: 0.000250 AC: 38AN: 152126Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000189 AC: 47AN: 248682Hom.: 0 AF XY: 0.000163 AC XY: 22AN XY: 134892
GnomAD4 exome AF: 0.000363 AC: 531AN: 1461320Hom.: 0 AF XY: 0.000362 AC XY: 263AN XY: 726918
GnomAD4 genome AF: 0.000250 AC: 38AN: 152126Hom.: 0 Cov.: 32 AF XY: 0.000188 AC XY: 14AN XY: 74316
ClinVar
Submissions by phenotype
not provided Uncertain:2Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Aug 01, 2023 | NEB: BP3 - |
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Nov 02, 2021 | In-frame deletion of 2 amino acids in a non-repeat region; In silico analysis supports a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge - |
Uncertain significance, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Sep 07, 2023 | - - |
Nemaline myopathy 2 Uncertain:2
Uncertain significance, no assertion criteria provided | clinical testing | Natera, Inc. | Sep 16, 2020 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Nov 01, 2022 | This variant, c.5698_5703del, results in the deletion of 2 amino acid(s) of the NEB protein (p.Tyr1900_Asn1901del), but otherwise preserves the integrity of the reading frame. This variant is present in population databases (rs775531807, gnomAD 0.04%). This variant has not been reported in the literature in individuals affected with NEB-related conditions. ClinVar contains an entry for this variant (Variation ID: 449072). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Nemaline myopathy 2;C5543431:Arthrogryposis multiplex congenita 6 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Feb 18, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at