rs886038449
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 4P and 3B. PM2PM5BP4_ModerateBP6
The NM_001164507.2(NEB):c.23185G>A(p.Ala7729Thr) variant causes a missense change. The variant allele was found at a frequency of 0.0000292 in 1,610,306 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A7729V) has been classified as Uncertain significance.
Frequency
Consequence
NM_001164507.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NEB | NM_001164507.2 | c.23185G>A | p.Ala7729Thr | missense_variant | 160/182 | ENST00000427231.7 | |
NEB | NM_001164508.2 | c.23185G>A | p.Ala7729Thr | missense_variant | 160/182 | ENST00000397345.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NEB | ENST00000397345.8 | c.23185G>A | p.Ala7729Thr | missense_variant | 160/182 | 5 | NM_001164508.2 | P5 | |
NEB | ENST00000427231.7 | c.23185G>A | p.Ala7729Thr | missense_variant | 160/182 | 5 | NM_001164507.2 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000460 AC: 7AN: 152114Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000123 AC: 3AN: 243684Hom.: 0 AF XY: 0.00000758 AC XY: 1AN XY: 131850
GnomAD4 exome AF: 0.0000274 AC: 40AN: 1458192Hom.: 0 Cov.: 30 AF XY: 0.0000290 AC XY: 21AN XY: 724822
GnomAD4 genome ? AF: 0.0000460 AC: 7AN: 152114Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74294
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 24, 2023 | The c.18082G>A (p.A6028T) alteration is located in exon 133 (coding exon 131) of the NEB gene. This alteration results from a G to A substitution at nucleotide position 18082, causing the alanine (A) at amino acid position 6028 to be replaced by a threonine (T). 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 | Mar 02, 2020 | - - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at