chr2-151671063-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6BS1BS2_Supporting
The NM_001164507.2(NEB):c.4466G>A(p.Gly1489Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000322 in 1,613,918 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict 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. G1489V) has been classified as Uncertain significance.
Frequency
Consequence
NM_001164507.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NEB | NM_001164507.2 | c.4466G>A | p.Gly1489Asp | missense_variant | 38/182 | ENST00000427231.7 | |
NEB | NM_001164508.2 | c.4466G>A | p.Gly1489Asp | missense_variant | 38/182 | ENST00000397345.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NEB | ENST00000397345.8 | c.4466G>A | p.Gly1489Asp | missense_variant | 38/182 | 5 | NM_001164508.2 | P5 | |
NEB | ENST00000427231.7 | c.4466G>A | p.Gly1489Asp | missense_variant | 38/182 | 5 | NM_001164507.2 | A2 | |
NEB | ENST00000409198.5 | c.4466G>A | p.Gly1489Asp | missense_variant | 38/150 | 5 | |||
NEB | ENST00000484968.1 | n.318G>A | non_coding_transcript_exon_variant | 1/3 | 4 |
Frequencies
GnomAD3 genomes AF: 0.00149 AC: 226AN: 152134Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000381 AC: 95AN: 249258Hom.: 0 AF XY: 0.000251 AC XY: 34AN XY: 135216
GnomAD4 exome AF: 0.000200 AC: 293AN: 1461666Hom.: 3 Cov.: 34 AF XY: 0.000169 AC XY: 123AN XY: 727116
GnomAD4 genome AF: 0.00149 AC: 227AN: 152252Hom.: 1 Cov.: 32 AF XY: 0.00149 AC XY: 111AN XY: 74458
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jan 15, 2019 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | May 08, 2017 | - - |
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Dec 28, 2015 | - - |
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Nemaline myopathy 2 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at