2-151600569-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_StrongBP6
The NM_001164507.2(NEB):c.13661G>A(p.Ser4554Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 12/17 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. S4554S) has been classified as Likely benign.
Frequency
Consequence
NM_001164507.2 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NEB | NM_001164507.2 | c.13661G>A | p.Ser4554Asn | missense_variant | 89/182 | ENST00000427231.7 | |
NEB | NM_001164508.2 | c.13661G>A | p.Ser4554Asn | missense_variant | 89/182 | ENST00000397345.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NEB | ENST00000397345.8 | c.13661G>A | p.Ser4554Asn | missense_variant | 89/182 | 5 | NM_001164508.2 | P5 | |
NEB | ENST00000427231.7 | c.13661G>A | p.Ser4554Asn | missense_variant | 89/182 | 5 | NM_001164507.2 | A2 | |
NEB | ENST00000409198.5 | c.11601+9240G>A | intron_variant | 5 |
Frequencies
GnomAD3 genomes Cov.: 0
GnomAD3 exomes AF: 0.000108 AC: 1AN: 9228Hom.: 0 AF XY: 0.000192 AC XY: 1AN XY: 5212
GnomAD4 exome Cov.: 0
GnomAD4 genome Cov.: 0
ClinVar
Submissions by phenotype
Nemaline myopathy 2 Uncertain:1Benign:1
Likely benign, no assertion criteria provided | clinical testing | Natera, Inc. | Nov 11, 2019 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Jan 03, 2018 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 19, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at