rs187977960
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 2P and 9B. PM2BP4_StrongBP6BS1
The NM_001164508.2(NEB):c.21673A>T(p.Thr7225Ser) variant causes a missense change. The variant allele was found at a frequency of 0.000172 in 1,613,642 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).
Frequency
Consequence
NM_001164508.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NEB | ENST00000397345.8 | c.21673A>T | p.Thr7225Ser | missense_variant | Exon 146 of 182 | 5 | NM_001164508.2 | ENSP00000380505.3 | ||
NEB | ENST00000427231.7 | c.21673A>T | p.Thr7225Ser | missense_variant | Exon 146 of 182 | 5 | NM_001164507.2 | ENSP00000416578.2 |
Frequencies
GnomAD3 genomes AF: 0.000966 AC: 147AN: 152196Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000197 AC: 49AN: 249144Hom.: 0 AF XY: 0.000200 AC XY: 27AN XY: 135162
GnomAD4 exome AF: 0.0000890 AC: 130AN: 1461328Hom.: 0 Cov.: 30 AF XY: 0.0000908 AC XY: 66AN XY: 726972
GnomAD4 genome AF: 0.000965 AC: 147AN: 152314Hom.: 0 Cov.: 32 AF XY: 0.000913 AC XY: 68AN XY: 74486
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.16570A>T (p.T5524S) alteration is located in exon 119 (coding exon 117) of the NEB gene. This alteration results from a A to T substitution at nucleotide position 16570, causing the threonine (T) at amino acid position 5524 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
NEB-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
not provided Benign:1
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Nemaline myopathy 2 Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at