X-137030150-A-G
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Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM4BP6_ModerateBS2
The NM_054021.2(GPR101):āc.1525T>Cā(p.Ter509Argext*?) variant causes a stop lost change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000376 in 1,170,327 control chromosomes in the GnomAD database, including 1 homozygotes. There are 6 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Genomes: š 0.000027 ( 0 hom., 0 hem., cov: 23)
Exomes š: 0.000039 ( 1 hom. 6 hem. )
Consequence
GPR101
NM_054021.2 stop_lost
NM_054021.2 stop_lost
Scores
1
4
Clinical Significance
Conservation
PhyloP100: 3.28
Genes affected
GPR101 (HGNC:14963): (G protein-coupled receptor 101) The protein encoded by this gene is an orphan G protein-coupled receptor of unknown function. The encoded protein is a member of a family of proteins that contain seven transmembrane domains and transduce extracellular signals through heterotrimeric G proteins. [provided by RefSeq, Sep 2011]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
PM4
Stoplost variant in NM_054021.2 Downstream stopcodon found after 538 codons.
BP6
Variant X-137030150-A-G is Benign according to our data. Variant chrX-137030150-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 722009.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High Hemizygotes in GnomAdExome4 at 6 XL gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GPR101 | NM_054021.2 | c.1525T>C | p.Ter509Argext*? | stop_lost | 2/2 | ENST00000651716.2 | NP_473362.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GPR101 | ENST00000651716.2 | c.1525T>C | p.Ter509Argext*? | stop_lost | 2/2 | NM_054021.2 | ENSP00000498972.1 | |||
ENSG00000291054 | ENST00000693626.2 | n.394-30375A>G | intron_variant |
Frequencies
GnomAD3 genomes AF: 0.0000267 AC: 3AN: 112303Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34443
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GnomAD3 exomes AF: 0.000253 AC: 37AN: 146509Hom.: 1 AF XY: 0.000106 AC XY: 5AN XY: 47181
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GnomAD4 exome AF: 0.0000388 AC: 41AN: 1057971Hom.: 1 Cov.: 29 AF XY: 0.0000176 AC XY: 6AN XY: 341721
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GnomAD4 genome AF: 0.0000267 AC: 3AN: 112356Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34506
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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 | Jun 06, 2018 | - - |
Computational scores
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BayesDel_addAF
Benign
T
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Benign
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Benign
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Benign
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Vest4
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at