5-177992754-A-C
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Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7
The NM_006261.5(PROP1):āc.636T>Gā(p.Pro212=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ). Synonymous variant affecting the same amino acid position (i.e. P212P) has been classified as Likely benign.
Frequency
Genomes: š 0.00011 ( 0 hom., cov: 0)
Exomes š: 0.0000034 ( 0 hom. )
Consequence
PROP1
NM_006261.5 synonymous
NM_006261.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.371
Genes affected
PROP1 (HGNC:9455): (PROP paired-like homeobox 1) This gene encodes a paired-like homeodomain transcription factor in the developing pituitary gland. Expression occurs prior to and is required for expression of pou domain transcription factor 1, which is responsible for pituitary development and hormone expression. Mutations in this gene have been associated with combined pituitary hormone deficiency-2 as well as deficiencies in luteinizing hormone, follicle-stimulating hormone, growth hormone, prolactin, and thyroid-stimulating hormone. [provided by RefSeq, Sep 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -7 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BP6
Variant 5-177992754-A-C is Benign according to our data. Variant chr5-177992754-A-C is described in ClinVar as [Likely_benign]. Clinvar id is 1587740.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.371 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PROP1 | NM_006261.5 | c.636T>G | p.Pro212= | synonymous_variant | 3/3 | ENST00000308304.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PROP1 | ENST00000308304.2 | c.636T>G | p.Pro212= | synonymous_variant | 3/3 | 1 | NM_006261.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000107 AC: 2AN: 18732Hom.: 0 Cov.: 0
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GnomAD4 exome AF: 0.00000341 AC: 1AN: 293136Hom.: 0 Cov.: 16 AF XY: 0.00 AC XY: 0AN XY: 151072
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GnomAD4 genome AF: 0.000107 AC: 2AN: 18772Hom.: 0 Cov.: 0 AF XY: 0.000110 AC XY: 1AN XY: 9112
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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 | Nov 18, 2021 | - - |
Computational scores
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BayesDel_noAF
Benign
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Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at