rs6166
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The ENST00000406846.7(FSHR):c.2039G>A(p.Ser680Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.558 in 1,613,272 control chromosomes in the GnomAD database, including 252,236 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
ENST00000406846.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FSHR | NM_000145.4 | c.2039G>A | p.Ser680Asn | missense_variant | 10/10 | ENST00000406846.7 | NP_000136.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FSHR | ENST00000406846.7 | c.2039G>A | p.Ser680Asn | missense_variant | 10/10 | 1 | NM_000145.4 | ENSP00000384708 | P1 | |
FSHR | ENST00000304421.8 | c.1961G>A | p.Ser654Asn | missense_variant | 9/9 | 1 | ENSP00000306780 | |||
ENST00000634588.1 | n.492+16377C>T | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.568 AC: 86242AN: 151908Hom.: 24645 Cov.: 32
GnomAD3 exomes AF: 0.574 AC: 144230AN: 251060Hom.: 41947 AF XY: 0.569 AC XY: 77131AN XY: 135650
GnomAD4 exome AF: 0.557 AC: 813884AN: 1461246Hom.: 227584 Cov.: 48 AF XY: 0.555 AC XY: 403744AN XY: 726958
GnomAD4 genome AF: 0.568 AC: 86292AN: 152026Hom.: 24652 Cov.: 32 AF XY: 0.567 AC XY: 42132AN XY: 74322
ClinVar
Submissions by phenotype
Ovarian hyperstimulation syndrome Benign:3
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Aug 10, 2021 | - - |
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Apr 27, 2017 | This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases was too high to be consistent with this variant causing disease. Therefore, this variant is classified as benign. - |
Benign, no assertion criteria provided | literature only | OMIM | Aug 01, 2005 | - - |
Ovarian dysgenesis 1 Benign:2
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Aug 10, 2021 | - - |
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Apr 27, 2017 | This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to rule this variant out of causing disease. Therefore, this variant is classified as benign. - |
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 03, 2015 | This variant is associated with the following publications: (PMID: 21269619, 19403562, 20399696, 21546300, 23470615, 23139742, 23413141, 16574671, 25132286, 19550076, 20817169, 20514429, 23536150, 24970684, 24718625, 21680247, 18159088, 15886248, 26905078, 29683332, 28282771, 25526787, 28547204) - |
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at