chrX-152850269-A-G
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_015922.3(NSDHL):āc.113A>Gā(p.Lys38Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000125 in 1,208,409 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 42 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Consequence
NM_015922.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NSDHL | NM_015922.3 | c.113A>G | p.Lys38Arg | missense_variant | 3/8 | ENST00000370274.8 | |
NSDHL | NM_001129765.2 | c.113A>G | p.Lys38Arg | missense_variant | 4/9 | ||
NSDHL | XM_017029564.2 | c.161A>G | p.Lys54Arg | missense_variant | 3/8 | ||
NSDHL | XM_011531178.3 | c.113A>G | p.Lys38Arg | missense_variant | 5/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NSDHL | ENST00000370274.8 | c.113A>G | p.Lys38Arg | missense_variant | 3/8 | 1 | NM_015922.3 | P1 | |
NSDHL | ENST00000440023.5 | c.113A>G | p.Lys38Arg | missense_variant | 4/9 | 5 | P1 | ||
NSDHL | ENST00000432467.1 | c.113A>G | p.Lys38Arg | missense_variant | 4/8 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000891 AC: 10AN: 112171Hom.: 0 Cov.: 23 AF XY: 0.000146 AC XY: 5AN XY: 34333
GnomAD3 exomes AF: 0.000240 AC: 44AN: 183452Hom.: 0 AF XY: 0.000147 AC XY: 10AN XY: 67902
GnomAD4 exome AF: 0.000129 AC: 141AN: 1096184Hom.: 0 Cov.: 29 AF XY: 0.000102 AC XY: 37AN XY: 361884
GnomAD4 genome AF: 0.0000891 AC: 10AN: 112225Hom.: 0 Cov.: 23 AF XY: 0.000145 AC XY: 5AN XY: 34397
ClinVar
Submissions by phenotype
NSDHL-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | May 16, 2023 | 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
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Aug 10, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at