chrX-8535755-C-T
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_000216.4(ANOS1):c.1678G>A(p.Val560Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00022 in 1,210,346 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 91 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 14/20 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_000216.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ANOS1 | NM_000216.4 | c.1678G>A | p.Val560Ile | missense_variant | 12/14 | ENST00000262648.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ANOS1 | ENST00000262648.8 | c.1678G>A | p.Val560Ile | missense_variant | 12/14 | 1 | NM_000216.4 | P1 | |
ANOS1 | ENST00000481896.1 | n.223G>A | non_coding_transcript_exon_variant | 2/2 | 4 |
Frequencies
GnomAD3 genomes AF: 0.000240 AC: 27AN: 112363Hom.: 0 Cov.: 23 AF XY: 0.000260 AC XY: 9AN XY: 34549
GnomAD3 exomes AF: 0.000867 AC: 159AN: 183362Hom.: 1 AF XY: 0.000796 AC XY: 54AN XY: 67820
GnomAD4 exome AF: 0.000218 AC: 239AN: 1097929Hom.: 0 Cov.: 31 AF XY: 0.000226 AC XY: 82AN XY: 363285
GnomAD4 genome AF: 0.000240 AC: 27AN: 112417Hom.: 0 Cov.: 23 AF XY: 0.000260 AC XY: 9AN XY: 34613
ClinVar
Submissions by phenotype
Hypogonadotropic hypogonadism 1 with or without anosmia Uncertain:2Benign:1
Uncertain significance, criteria provided, single submitter | clinical testing | Mendelics | May 28, 2019 | - - |
Uncertain significance, criteria provided, single submitter | reference population | Soonchunhyang University Bucheon Hospital, Soonchunhyang University Medical Center | Mar 18, 2016 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 04, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at