rs809446
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6_Very_StrongBP7
The NM_000216.4(ANOS1):c.1833C>T(p.Ile611=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.53 ( 12116 hom., 17436 hem., cov: 23)
Exomes 𝑓: 0.62 ( 147868 hom. 220049 hem. )
Failed GnomAD Quality Control
Consequence
ANOS1
NM_000216.4 synonymous
NM_000216.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.356
Genes affected
ANOS1 (HGNC:6211): (anosmin 1) Mutations in this gene cause the X-linked Kallmann syndrome. The encoded protein is similar in sequence to proteins known to function in neural cell adhesion and axonal migration. In addition, this cell surface protein is N-glycosylated and may have anti-protease activity. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.53).
BP6
?
Variant X-8535600-G-A is Benign according to our data. Variant chrX-8535600-G-A is described in ClinVar as [Benign]. Clinvar id is 255564.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-8535600-G-A is described in Lovd as [Benign]. Variant chrX-8535600-G-A is described in Lovd as [Likely_benign].
BP7
?
Synonymous conserved (PhyloP=-0.356 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ANOS1 | NM_000216.4 | c.1833C>T | p.Ile611= | synonymous_variant | 12/14 | ENST00000262648.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ANOS1 | ENST00000262648.8 | c.1833C>T | p.Ile611= | synonymous_variant | 12/14 | 1 | NM_000216.4 | P1 | |
ANOS1 | ENST00000481896.1 | n.378C>T | non_coding_transcript_exon_variant | 2/2 | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.535 AC: 59407AN: 110963Hom.: 12123 Cov.: 23 AF XY: 0.525 AC XY: 17430AN XY: 33225
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GnomAD3 exomes AF: 0.555 AC: 100457AN: 180887Hom.: 18903 AF XY: 0.559 AC XY: 36673AN XY: 65621
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GnomAD4 exome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.624 AC: 680341AN: 1090675Hom.: 147868 Cov.: 29 AF XY: 0.616 AC XY: 220049AN XY: 357275
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GnomAD4 genome ? Data not reliable, filtered out with message: InbreedingCoeff AF: 0.535 AC: 59394AN: 111017Hom.: 12116 Cov.: 23 AF XY: 0.524 AC XY: 17436AN XY: 33289
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ClinVar
Significance: Benign
Submissions summary: Benign:8
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:5
Benign, no assertion criteria provided | clinical testing | Clinical Genetics, Academic Medical Center | - | - - |
Benign, no assertion criteria provided | clinical testing | Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen | - | - - |
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Benign, no assertion criteria provided | clinical testing | Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ | - | - - |
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Jul 27, 2017 | - - |
Hypogonadotropic hypogonadism 1 with or without anosmia Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Aug 19, 2021 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 03, 2015 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at