chr3-133807811-C-T
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_ModerateBP6_ModerateBP7BS1BS2
The NM_001379313.1(SRPRB):c.315C>T(p.Val105=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00244 in 1,609,990 control chromosomes in the GnomAD database, including 82 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.013 ( 47 hom., cov: 32)
Exomes 𝑓: 0.0014 ( 35 hom. )
Consequence
SRPRB
NM_001379313.1 synonymous
NM_001379313.1 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.05
Genes affected
SRPRB (HGNC:24085): (SRP receptor subunit beta) The protein encoded by this gene has similarity to mouse protein which is a subunit of the signal recognition particle receptor (SR). This subunit is a transmembrane GTPase belonging to the GTPase superfamily. It anchors alpha subunit, a peripheral membrane GTPase, to the ER membrane. SR is required for the cotranslational targeting of both secretory and membrane proteins to the ER membrane. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.3).
BP6
?
Variant 3-133807811-C-T is Benign according to our data. Variant chr3-133807811-C-T is described in ClinVar as [Benign]. Clinvar id is 785065.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=1.05 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0126 (1915/152198) while in subpopulation AFR AF= 0.0433 (1798/41514). AF 95% confidence interval is 0.0416. There are 47 homozygotes in gnomad4. There are 879 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 48 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SRPRB | NM_001379313.1 | c.315C>T | p.Val105= | synonymous_variant | 3/7 | ENST00000678299.1 | |
SRPRB | NM_021203.4 | c.315C>T | p.Val105= | synonymous_variant | 4/8 | ||
SRPRB | NR_163491.1 | n.349C>T | non_coding_transcript_exon_variant | 3/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SRPRB | ENST00000678299.1 | c.315C>T | p.Val105= | synonymous_variant | 3/7 | NM_001379313.1 | P1 | ||
SRPRB | ENST00000466490.7 | c.315C>T | p.Val105= | synonymous_variant | 4/8 | 5 | P1 | ||
SRPRB | ENST00000494297.5 | n.217C>T | non_coding_transcript_exon_variant | 2/6 | 2 | ||||
SRPRB | ENST00000484684.1 | downstream_gene_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0126 AC: 1912AN: 152080Hom.: 48 Cov.: 32
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GnomAD3 exomes AF: 0.00324 AC: 800AN: 247202Hom.: 16 AF XY: 0.00225 AC XY: 301AN XY: 133780
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GnomAD4 exome AF: 0.00138 AC: 2008AN: 1457792Hom.: 35 Cov.: 29 AF XY: 0.00116 AC XY: 840AN XY: 725318
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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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