X-8536792-C-T
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBP6_Very_Strong
The ENST00000262648.8(ANOS1):c.1600G>A(p.Val534Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.55 ( 12445 hom., 17498 hem., cov: 23)
Exomes 𝑓: 0.63 ( 149723 hom. 224115 hem. )
Failed GnomAD Quality Control
Consequence
ANOS1
ENST00000262648.8 missense
ENST00000262648.8 missense
Scores
16
Clinical Significance
Conservation
PhyloP100: -0.456
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 -12 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=3.1132084E-5).
BP6
Variant X-8536792-C-T is Benign according to our data. Variant chrX-8536792-C-T is described in ClinVar as [Benign]. Clinvar id is 255563.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-8536792-C-T is described in Lovd as [Benign]. Variant chrX-8536792-C-T is described in Lovd as [Likely_benign].
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ANOS1 | NM_000216.4 | c.1600G>A | p.Val534Ile | missense_variant | 11/14 | ENST00000262648.8 | NP_000207.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ANOS1 | ENST00000262648.8 | c.1600G>A | p.Val534Ile | missense_variant | 11/14 | 1 | NM_000216.4 | ENSP00000262648 | P1 | |
ANOS1 | ENST00000481896.1 | n.145G>A | non_coding_transcript_exon_variant | 1/2 | 4 |
Frequencies
GnomAD3 genomes AF: 0.546 AC: 60238AN: 110304Hom.: 12452 Cov.: 23 AF XY: 0.537 AC XY: 17484AN XY: 32584
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GnomAD3 exomes AF: 0.559 AC: 98770AN: 176751Hom.: 19112 AF XY: 0.559 AC XY: 34599AN XY: 61855
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GnomAD4 exome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.628 AC: 687969AN: 1094888Hom.: 149723 Cov.: 33 AF XY: 0.621 AC XY: 224115AN XY: 360740
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GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.546 AC: 60233AN: 110357Hom.: 12445 Cov.: 23 AF XY: 0.536 AC XY: 17498AN XY: 32647
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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:4
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Jul 27, 2017 | - - |
Benign, no assertion criteria provided | clinical testing | Clinical Genetics, Academic Medical Center | - | - - |
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Benign, no assertion criteria provided | clinical testing | Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen | - | - - |
Hypogonadotropic hypogonadism 1 with or without anosmia Benign:2
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Aug 19, 2021 | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 31, 2024 | - - |
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 03, 2015 | - - |
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
DEOGEN2
Benign
T
FATHMM_MKL
Benign
N
LIST_S2
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Benign
N
MutationTaster
Benign
P
PrimateAI
Benign
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Benign
T
Sift4G
Benign
T
Polyphen
B
Vest4
MPC
ClinPred
T
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gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at