rs199771303
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_ModerateBP6BS1BS2
The NM_000216.4(ANOS1):āc.2015A>Gā(p.His672Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000287 in 1,170,607 control chromosomes in the GnomAD database, including 1 homozygotes. There are 112 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_000216.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ANOS1 | NM_000216.4 | c.2015A>G | p.His672Arg | missense_variant | 14/14 | ENST00000262648.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ANOS1 | ENST00000262648.8 | c.2015A>G | p.His672Arg | missense_variant | 14/14 | 1 | NM_000216.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000401 AC: 45AN: 112356Hom.: 0 Cov.: 22 AF XY: 0.000464 AC XY: 16AN XY: 34506
GnomAD3 exomes AF: 0.000280 AC: 51AN: 181953Hom.: 0 AF XY: 0.000255 AC XY: 17AN XY: 66615
GnomAD4 exome AF: 0.000275 AC: 291AN: 1058201Hom.: 1 Cov.: 23 AF XY: 0.000290 AC XY: 96AN XY: 331339
GnomAD4 genome ? AF: 0.000400 AC: 45AN: 112406Hom.: 0 Cov.: 22 AF XY: 0.000463 AC XY: 16AN XY: 34566
ClinVar
Submissions by phenotype
Hypogonadotropic hypogonadism 1 with or without anosmia Uncertain:1Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Oct 03, 2023 | - - |
Uncertain significance, criteria provided, single submitter | research | Lupski Lab, Baylor-Hopkins CMG, Baylor College of Medicine | - | - - |
Amenorrhea Uncertain:1
Uncertain significance, no assertion criteria provided | literature only | Yale Center for Mendelian Genomics, Yale University | Mar 08, 2021 | - - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 05, 2016 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at