X-17376088-TCGGCGGCGG-TCGGCGGCGGCGG
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP6_Very_StrongBS2
The NM_001291867.2(NHS):c.348_350dupGGC(p.Ala117dup) variant causes a disruptive inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00013 in 1,078,419 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 36 hemizygotes in GnomAD. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001291867.2 disruptive_inframe_insertion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NHS | NM_001291867.2 | c.348_350dupGGC | p.Ala117dup | disruptive_inframe_insertion | Exon 1 of 9 | ENST00000676302.1 | NP_001278796.1 | |
NHS | NM_198270.4 | c.348_350dupGGC | p.Ala117dup | disruptive_inframe_insertion | Exon 1 of 8 | NP_938011.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NHS | ENST00000676302.1 | c.348_350dupGGC | p.Ala117dup | disruptive_inframe_insertion | Exon 1 of 9 | NM_001291867.2 | ENSP00000502262.1 | |||
NHS | ENST00000380060.7 | c.348_350dupGGC | p.Ala117dup | disruptive_inframe_insertion | Exon 1 of 8 | 1 | ENSP00000369400.3 |
Frequencies
GnomAD3 genomes AF: 0.000272 AC: 30AN: 110366Hom.: 0 Cov.: 23 AF XY: 0.000180 AC XY: 6AN XY: 33338
GnomAD3 exomes AF: 0.000246 AC: 8AN: 32481Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 7751
GnomAD4 exome AF: 0.000114 AC: 110AN: 968013Hom.: 0 Cov.: 31 AF XY: 0.0000977 AC XY: 30AN XY: 306963
GnomAD4 genome AF: 0.000272 AC: 30AN: 110406Hom.: 0 Cov.: 23 AF XY: 0.000180 AC XY: 6AN XY: 33392
ClinVar
Submissions by phenotype
Inborn genetic diseases Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Nance-Horan syndrome Benign:1
- -
not provided Benign:1
NHS: BS2 -
NHS-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). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at