chr2-151680765-C-G
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP6
The NM_001164507.2(NEB):āc.3007G>Cā(p.Val1003Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000527 in 1,612,822 control chromosomes in the GnomAD database, with no homozygous occurrence. 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). Synonymous variant affecting the same amino acid position (i.e. V1003V) has been classified as Likely benign.
Frequency
Consequence
NM_001164507.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NEB | NM_001164507.2 | c.3007G>C | p.Val1003Leu | missense_variant | 30/182 | ENST00000427231.7 | |
NEB | NM_001164508.2 | c.3007G>C | p.Val1003Leu | missense_variant | 30/182 | ENST00000397345.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NEB | ENST00000397345.8 | c.3007G>C | p.Val1003Leu | missense_variant | 30/182 | 5 | NM_001164508.2 | P5 | |
NEB | ENST00000427231.7 | c.3007G>C | p.Val1003Leu | missense_variant | 30/182 | 5 | NM_001164507.2 | A2 | |
NEB | ENST00000409198.5 | c.3007G>C | p.Val1003Leu | missense_variant | 30/150 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.000243 AC: 37AN: 152128Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000763 AC: 19AN: 249172Hom.: 0 AF XY: 0.0000444 AC XY: 6AN XY: 135172
GnomAD4 exome AF: 0.0000322 AC: 47AN: 1460576Hom.: 0 Cov.: 30 AF XY: 0.0000261 AC XY: 19AN XY: 726662
GnomAD4 genome ? AF: 0.000250 AC: 38AN: 152246Hom.: 0 Cov.: 32 AF XY: 0.000282 AC XY: 21AN XY: 74458
ClinVar
Submissions by phenotype
Nemaline myopathy 2 Uncertain:1Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 16, 2024 | - - |
Uncertain significance, no assertion criteria provided | clinical testing | Natera, Inc. | Nov 11, 2019 | - - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Jun 06, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at