X-17375806-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001291867.2(NHS):c.49C>T(p.Arg17Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000113 in 1,150,809 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 6 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Consequence
NM_001291867.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000889 AC: 1AN: 112536Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34736
GnomAD4 exome AF: 0.0000116 AC: 12AN: 1038273Hom.: 0 Cov.: 31 AF XY: 0.0000177 AC XY: 6AN XY: 339291
GnomAD4 genome AF: 0.00000889 AC: 1AN: 112536Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34736
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.49C>T (p.R17W) alteration is located in exon 1 (coding exon 1) of the NHS gene. This alteration results from a C to T substitution at nucleotide position 49, causing the arginine (R) at amino acid position 17 to be replaced by a tryptophan (W). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
not provided Uncertain:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at