rs376611641
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP6
The NM_001164507.2(NEB):c.3964G>T(p.Ala1322Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000297 in 1,613,826 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 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. A1322A) 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.3964G>T | p.Ala1322Ser | missense_variant | 36/182 | ENST00000427231.7 | |
NEB | NM_001164508.2 | c.3964G>T | p.Ala1322Ser | missense_variant | 36/182 | ENST00000397345.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NEB | ENST00000397345.8 | c.3964G>T | p.Ala1322Ser | missense_variant | 36/182 | 5 | NM_001164508.2 | P5 | |
NEB | ENST00000427231.7 | c.3964G>T | p.Ala1322Ser | missense_variant | 36/182 | 5 | NM_001164507.2 | A2 | |
NEB | ENST00000409198.5 | c.3964G>T | p.Ala1322Ser | missense_variant | 36/150 | 5 |
Frequencies
GnomAD3 genomes AF: 0.000158 AC: 24AN: 152200Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000321 AC: 8AN: 249248Hom.: 0 AF XY: 0.0000296 AC XY: 4AN XY: 135214
GnomAD4 exome AF: 0.0000164 AC: 24AN: 1461626Hom.: 0 Cov.: 30 AF XY: 0.0000179 AC XY: 13AN XY: 727106
GnomAD4 genome AF: 0.000158 AC: 24AN: 152200Hom.: 0 Cov.: 31 AF XY: 0.000121 AC XY: 9AN XY: 74364
ClinVar
Submissions by phenotype
Nemaline myopathy 2 Uncertain:1Benign:1
Uncertain significance, no assertion criteria provided | clinical testing | Natera, Inc. | Nov 11, 2019 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 18, 2024 | - - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Jun 27, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at