chr4-15707630-A-G
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_004334.3(BST1):āc.435A>Gā(p.Arg145=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000501 in 1,614,056 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Genomes: š 0.0025 ( 2 hom., cov: 31)
Exomes š: 0.00029 ( 3 hom. )
Consequence
BST1
NM_004334.3 synonymous
NM_004334.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.288
Genes affected
BST1 (HGNC:1118): (bone marrow stromal cell antigen 1) Bone marrow stromal cell antigen-1 is a stromal cell line-derived glycosylphosphatidylinositol-anchored molecule that facilitates pre-B-cell growth. The deduced amino acid sequence exhibits 33% similarity with CD38. BST1 expression is enhanced in bone marrow stromal cell lines derived from patients with rheumatoid arthritis. The polyclonal B-cell abnormalities in rheumatoid arthritis may be, at least in part, attributed to BST1 overexpression in the stromal cell population. [provided by RefSeq, Jul 2008]
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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=-0.74).
BP6
Variant 4-15707630-A-G is Benign according to our data. Variant chr4-15707630-A-G is described in ClinVar as [Benign]. Clinvar id is 717839.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.288 with no splicing effect.
BS2
High Homozygotes in GnomAd4 at 2 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BST1 | NM_004334.3 | c.435A>G | p.Arg145= | synonymous_variant | 3/9 | ENST00000265016.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BST1 | ENST00000265016.9 | c.435A>G | p.Arg145= | synonymous_variant | 3/9 | 1 | NM_004334.3 | P1 | |
BST1 | ENST00000382346.7 | c.480A>G | p.Arg160= | synonymous_variant | 4/10 | 5 | |||
BST1 | ENST00000505785.5 | c.123A>G | p.Arg41= | synonymous_variant | 1/7 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00251 AC: 382AN: 152100Hom.: 2 Cov.: 31
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GnomAD3 exomes AF: 0.000628 AC: 158AN: 251456Hom.: 1 AF XY: 0.000441 AC XY: 60AN XY: 135902
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GnomAD4 exome AF: 0.000291 AC: 425AN: 1461838Hom.: 3 Cov.: 32 AF XY: 0.000252 AC XY: 183AN XY: 727228
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GnomAD4 genome AF: 0.00252 AC: 383AN: 152218Hom.: 2 Cov.: 31 AF XY: 0.00226 AC XY: 168AN XY: 74434
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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 | Aug 20, 2018 | - - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at