chrX-8533287-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2
The NM_000216.4(ANOS1):c.1985-234G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00853 in 111,992 control chromosomes in the GnomAD database, including 10 homozygotes. There are 279 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0085 ( 10 hom., 279 hem., cov: 23)
Consequence
ANOS1
NM_000216.4 intron
NM_000216.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.278
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 -10 ACMG points.
BP6
?
Variant X-8533287-C-T is Benign according to our data. Variant chrX-8533287-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 1203979.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00853 (955/111992) while in subpopulation AFR AF= 0.0292 (901/30822). AF 95% confidence interval is 0.0276. There are 10 homozygotes in gnomad4. There are 279 alleles in male gnomad4 subpopulation. Median coverage is 23. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 10 XL,Digenic gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ANOS1 | NM_000216.4 | c.1985-234G>A | intron_variant | ENST00000262648.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ANOS1 | ENST00000262648.8 | c.1985-234G>A | intron_variant | 1 | NM_000216.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00855 AC: 957AN: 111943Hom.: 10 Cov.: 23 AF XY: 0.00818 AC XY: 279AN XY: 34109
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.00853 AC: 955AN: 111992Hom.: 10 Cov.: 23 AF XY: 0.00817 AC XY: 279AN XY: 34168
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 25, 2020 | - - |
Computational scores
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Name
Calibrated prediction
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
DS_AG_spliceai
Position offset: -30
Find out detailed SpliceAI scores and Pangolin per-transcript scores at