rs200523155
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP6
The NM_001164507.2(NEB):c.21173C>T(p.Thr7058Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000189 in 1,612,960 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).
Frequency
Consequence
NM_001164507.2 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
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.21173C>T | p.Thr7058Ile | missense_variant | 141/182 | ENST00000427231.7 | |
NEB | NM_001164508.2 | c.21173C>T | p.Thr7058Ile | missense_variant | 141/182 | ENST00000397345.8 | |
LOC124906081 | XR_007087266.1 | n.43-652G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NEB | ENST00000397345.8 | c.21173C>T | p.Thr7058Ile | missense_variant | 141/182 | 5 | NM_001164508.2 | P5 | |
NEB | ENST00000427231.7 | c.21173C>T | p.Thr7058Ile | missense_variant | 141/182 | 5 | NM_001164507.2 | A2 |
Frequencies
GnomAD3 genomes AF: 0.000138 AC: 21AN: 152156Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000181 AC: 45AN: 248540Hom.: 0 AF XY: 0.000163 AC XY: 22AN XY: 134820
GnomAD4 exome AF: 0.000194 AC: 284AN: 1460804Hom.: 0 Cov.: 29 AF XY: 0.000168 AC XY: 122AN XY: 726726
GnomAD4 genome AF: 0.000138 AC: 21AN: 152156Hom.: 0 Cov.: 32 AF XY: 0.000161 AC XY: 12AN XY: 74330
ClinVar
Submissions by phenotype
Nemaline myopathy 2 Uncertain:2Benign:1
Uncertain significance, criteria provided, single submitter | clinical testing | Daryl Scott Lab, Baylor College of Medicine | Feb 01, 2022 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 16, 2024 | - - |
Uncertain significance, no assertion criteria provided | clinical testing | Natera, Inc. | Jan 17, 2020 | - - |
not provided Uncertain:1Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 14, 2020 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Sep 10, 2020 | - - |
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 29, 2021 | The c.16070C>T (p.T5357I) alteration is located in exon 114 (coding exon 112) of the NEB gene. This alteration results from a C to T substitution at nucleotide position 16070, causing the threonine (T) at amino acid position 5357 to be replaced by an isoleucine (I). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at