11-30232049-C-T
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Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_001382289.1(FSHB):c.147C>T(p.Tyr49=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000682 in 1,613,770 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000013 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0000062 ( 0 hom. )
Consequence
FSHB
NM_001382289.1 synonymous
NM_001382289.1 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.227
Genes affected
FSHB (HGNC:3964): (follicle stimulating hormone subunit beta) The pituitary glycoprotein hormone family includes follicle-stimulating hormone, luteinizing hormone, chorionic gonadotropin, and thyroid-stimulating hormone. All of these glycoproteins consist of an identical alpha subunit and a hormone-specific beta subunit. This gene encodes the beta subunit of follicle-stimulating hormone. In conjunction with luteinizing hormone, follicle-stimulating hormone induces egg and sperm production. Alternative splicing results in two transcript variants encoding the same protein. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.45).
BP6
Variant 11-30232049-C-T is Benign according to our data. Variant chr11-30232049-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 1658041.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.227 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FSHB | NM_001382289.1 | c.147C>T | p.Tyr49= | synonymous_variant | 2/3 | ENST00000533718.2 | NP_001369218.1 | |
ARL14EP-DT | XR_007062639.1 | n.351+84841G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FSHB | ENST00000533718.2 | c.147C>T | p.Tyr49= | synonymous_variant | 2/3 | 1 | NM_001382289.1 | ENSP00000433424 | P1 | |
ARL14EP-DT | ENST00000662729.1 | n.293-75196G>A | intron_variant, non_coding_transcript_variant | |||||||
FSHB | ENST00000254122.8 | c.147C>T | p.Tyr49= | synonymous_variant | 2/3 | 5 | ENSP00000254122 | P1 | ||
FSHB | ENST00000417547.1 | c.147C>T | p.Tyr49= | synonymous_variant | 2/3 | 5 | ENSP00000416606 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152258Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251004Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135640
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GnomAD4 exome AF: 0.00000616 AC: 9AN: 1461512Hom.: 0 Cov.: 32 AF XY: 0.00000550 AC XY: 4AN XY: 727052
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GnomAD4 genome AF: 0.0000131 AC: 2AN: 152258Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74378
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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 | Labcorp Genetics (formerly Invitae), Labcorp | Dec 10, 2021 | - - |
Computational scores
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Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at