11-30233638-C-T
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_001382289.1(FSHB):c.228C>T(p.Tyr76Tyr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.468 in 1,613,528 control chromosomes in the GnomAD database, including 182,686 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001382289.1 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FSHB | NM_001382289.1 | c.228C>T | p.Tyr76Tyr | synonymous_variant | Exon 3 of 3 | ENST00000533718.2 | NP_001369218.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FSHB | ENST00000533718.2 | c.228C>T | p.Tyr76Tyr | synonymous_variant | Exon 3 of 3 | 1 | NM_001382289.1 | ENSP00000433424.1 | ||
FSHB | ENST00000254122.8 | c.228C>T | p.Tyr76Tyr | synonymous_variant | Exon 3 of 3 | 5 | ENSP00000254122.3 | |||
FSHB | ENST00000417547.1 | c.228C>T | p.Tyr76Tyr | synonymous_variant | Exon 3 of 3 | 5 | ENSP00000416606.1 | |||
ARL14EP-DT | ENST00000662729.1 | n.293-76785G>A | intron_variant | Intron 3 of 4 |
Frequencies
GnomAD3 genomes AF: 0.538 AC: 81711AN: 151874Hom.: 22969 Cov.: 32
GnomAD3 exomes AF: 0.512 AC: 128318AN: 250780Hom.: 33910 AF XY: 0.509 AC XY: 68947AN XY: 135502
GnomAD4 exome AF: 0.461 AC: 674149AN: 1461534Hom.: 159692 Cov.: 53 AF XY: 0.465 AC XY: 337836AN XY: 727090
GnomAD4 genome AF: 0.538 AC: 81780AN: 151994Hom.: 22994 Cov.: 32 AF XY: 0.543 AC XY: 40347AN XY: 74262
ClinVar
Submissions by phenotype
not provided Benign:3
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Hypogonadotropic hypogonadism 24 without anosmia Benign:2
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
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not specified Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at