5-35065803-A-G
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_000949.7(PRLR):c.1155T>C(p.Asn385=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000234 in 1,613,984 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000092 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00025 ( 6 hom. )
Consequence
PRLR
NM_000949.7 synonymous
NM_000949.7 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.441
Genes affected
PRLR (HGNC:9446): (prolactin receptor) This gene encodes a receptor for the anterior pituitary hormone, prolactin, and belongs to the type I cytokine receptor family. Prolactin-dependent signaling occurs as the result of ligand-induced dimerization of the prolactin receptor. Several alternatively spliced transcript variants encoding different membrane-bound and soluble isoforms have been described for this gene, which may function to modulate the endocrine and autocrine effects of prolactin in normal tissue and cancer. [provided by RefSeq, Feb 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BP6
?
Variant 5-35065803-A-G is Benign according to our data. Variant chr5-35065803-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 3044456.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-0.441 with no splicing effect.
BS2
?
High AC in GnomAd at 14 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRLR | NM_000949.7 | c.1155T>C | p.Asn385= | synonymous_variant | 10/10 | ENST00000618457.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRLR | ENST00000618457.5 | c.1155T>C | p.Asn385= | synonymous_variant | 10/10 | 1 | NM_000949.7 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000921 AC: 14AN: 151982Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000533 AC: 134AN: 251406Hom.: 3 AF XY: 0.000787 AC XY: 107AN XY: 135876
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GnomAD4 exome AF: 0.000249 AC: 364AN: 1461884Hom.: 6 Cov.: 31 AF XY: 0.000407 AC XY: 296AN XY: 727242
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GnomAD4 genome ? AF: 0.0000920 AC: 14AN: 152100Hom.: 0 Cov.: 32 AF XY: 0.000148 AC XY: 11AN XY: 74344
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
PRLR-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jun 07, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
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