rs901588590
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2
The NM_001136200.2(BORCS7):c.130C>A(p.Arg44Arg) variant causes a synonymous change. The variant allele was found at a frequency of 0.000000721 in 1,387,568 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 31)
Exomes 𝑓: 7.2e-7 ( 0 hom. )
Consequence
BORCS7
NM_001136200.2 synonymous
NM_001136200.2 synonymous
Scores
1
1
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 6.82
Publications
0 publications found
Genes affected
BORCS7 (HGNC:23516): (BLOC-1 related complex subunit 7) Part of BORC complex. [provided by Alliance of Genome Resources, Apr 2022]
BORCS7-ASMT (HGNC:49183): (BORCS7-ASMT readthrough (NMD candidate)) This locus represents naturally occurring read-through transcription between the neighboring C10orf32 (chromosome 10 open reading frame 32) and AS3MT (arsenic, +3 oxidation state, methyltransferase) genes. The read-through transcript is a candidate for nonsense-mediated mRNA decay (NMD), and is therefore unlikely to produce a protein product. [provided by RefSeq, Dec 2010]
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| BORCS7 | NM_001136200.2 | c.130C>A | p.Arg44Arg | synonymous_variant | Exon 1 of 5 | ENST00000339834.10 | NP_001129672.1 | |
| BORCS7 | NM_144591.5 | c.130C>A | p.Arg44Arg | synonymous_variant | Exon 1 of 6 | NP_653192.2 | ||
| BORCS7-ASMT | NR_037644.1 | n.207C>A | non_coding_transcript_exon_variant | Exon 1 of 15 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| BORCS7 | ENST00000339834.10 | c.130C>A | p.Arg44Arg | synonymous_variant | Exon 1 of 5 | 1 | NM_001136200.2 | ENSP00000342331.5 | ||
| BORCS7-ASMT | ENST00000299353.6 | n.130C>A | non_coding_transcript_exon_variant | Exon 1 of 15 | 5 | ENSP00000299353.5 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
31
GnomAD4 exome AF: 7.21e-7 AC: 1AN: 1387568Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 681060 show subpopulations
GnomAD4 exome
AF:
AC:
1
AN:
1387568
Hom.:
Cov.:
30
AF XY:
AC XY:
0
AN XY:
681060
show subpopulations
African (AFR)
AF:
AC:
0
AN:
31652
American (AMR)
AF:
AC:
0
AN:
35596
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
25078
East Asian (EAS)
AF:
AC:
0
AN:
35688
South Asian (SAS)
AF:
AC:
1
AN:
79110
European-Finnish (FIN)
AF:
AC:
0
AN:
49138
Middle Eastern (MID)
AF:
AC:
0
AN:
5444
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1068480
Other (OTH)
AF:
AC:
0
AN:
57382
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.575
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
GnomAD4 genome
Cov.:
31
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Uncertain
DANN
Benign
PhyloP100
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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