rs587780403
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_001291867.2(NHS):c.2047G>A(p.Val683Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000355 in 1,210,384 control chromosomes in the GnomAD database, including 1 homozygotes. There are 12 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 12/17 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_001291867.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NHS | NM_001291867.2 | c.2047G>A | p.Val683Met | missense_variant | 7/9 | ENST00000676302.1 | NP_001278796.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NHS | ENST00000676302.1 | c.2047G>A | p.Val683Met | missense_variant | 7/9 | NM_001291867.2 | ENSP00000502262.1 |
Frequencies
GnomAD3 genomes AF: 0.0000357 AC: 4AN: 112081Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 34255
GnomAD3 exomes AF: 0.0000546 AC: 10AN: 183299Hom.: 0 AF XY: 0.0000295 AC XY: 2AN XY: 67759
GnomAD4 exome AF: 0.0000355 AC: 39AN: 1098248Hom.: 1 Cov.: 33 AF XY: 0.0000330 AC XY: 12AN XY: 363602
GnomAD4 genome AF: 0.0000357 AC: 4AN: 112136Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 34320
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Dec 11, 2013 | - - |
Nance-Horan syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 11, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at