chrX-17375755-G-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001291867.2(NHS):c.-3G>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001291867.2 5_prime_UTR_premature_start_codon_gain
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NHS | NM_001291867.2 | c.-3G>T | 5_prime_UTR_premature_start_codon_gain_variant | Exon 1 of 9 | ENST00000676302.1 | NP_001278796.1 | ||
NHS | NM_001291867.2 | c.-3G>T | 5_prime_UTR_variant | Exon 1 of 9 | ENST00000676302.1 | NP_001278796.1 | ||
NHS | NM_198270.4 | c.-3G>T | 5_prime_UTR_premature_start_codon_gain_variant | Exon 1 of 8 | NP_938011.1 | |||
NHS | NM_198270.4 | c.-3G>T | 5_prime_UTR_variant | Exon 1 of 8 | NP_938011.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NHS | ENST00000676302 | c.-3G>T | 5_prime_UTR_premature_start_codon_gain_variant | Exon 1 of 9 | NM_001291867.2 | ENSP00000502262.1 | ||||
NHS | ENST00000380060 | c.-3G>T | 5_prime_UTR_premature_start_codon_gain_variant | Exon 1 of 8 | 1 | ENSP00000369400.3 | ||||
NHS | ENST00000676302 | c.-3G>T | 5_prime_UTR_variant | Exon 1 of 9 | NM_001291867.2 | ENSP00000502262.1 | ||||
NHS | ENST00000380060 | c.-3G>T | 5_prime_UTR_variant | Exon 1 of 8 | 1 | ENSP00000369400.3 |
Frequencies
GnomAD3 genomes Cov.: 23
GnomAD4 exome Cov.: 31
GnomAD4 genome Cov.: 23
ClinVar
Submissions by phenotype
not provided Uncertain:1
Not observed at significant frequency in large population cohorts (gnomAD); Has not been previously published as pathogenic or benign to our knowledge -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.