10-102862895-C-G

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_001136200.2(BORCS7):ā€‹c.292C>Gā€‹(p.Gln98Glu) variant causes a missense change. The variant allele was found at a frequency of 0.0000048 in 1,458,574 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 11/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā˜…).

Frequency

Genomes: not found (cov: 32)
Exomes š‘“: 0.0000048 ( 0 hom. )

Consequence

BORCS7
NM_001136200.2 missense

Scores

1
1
14

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 4.68
Variant links:
Genes affected
BORCS7 (HGNC:23516): (BLOC-1 related complex subunit 7) Part of BORC complex. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.12588191).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
BORCS7NM_001136200.2 linkuse as main transcriptc.292C>G p.Gln98Glu missense_variant 5/5 ENST00000339834.10
BORCS7-ASMTNR_037644.1 linkuse as main transcriptn.369C>G non_coding_transcript_exon_variant 5/15
BORCS7NM_144591.5 linkuse as main transcriptc.292C>G p.Gln98Glu missense_variant 5/6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
BORCS7ENST00000339834.10 linkuse as main transcriptc.292C>G p.Gln98Glu missense_variant 5/51 NM_001136200.2 P1
BORCS7ENST00000369883.3 linkuse as main transcriptc.292C>G p.Gln98Glu missense_variant 5/61 P1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD3 exomes
AF:
0.0000280
AC:
7
AN:
249844
Hom.:
0
AF XY:
0.0000222
AC XY:
3
AN XY:
135246
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.000202
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.00000480
AC:
7
AN:
1458574
Hom.:
0
Cov.:
29
AF XY:
0.00000413
AC XY:
3
AN XY:
725860
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.000157
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
32
Bravo
AF:
0.0000113
ExAC
AF:
0.0000330
AC:
4

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsDec 16, 2022The c.292C>G (p.Q98E) alteration is located in exon 5 (coding exon 5) of the BORCS7 gene. This alteration results from a C to G substitution at nucleotide position 292, causing the glutamine (Q) at amino acid position 98 to be replaced by a glutamic acid (E). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.12
BayesDel_addAF
Benign
-0.19
T
BayesDel_noAF
Benign
-0.23
CADD
Uncertain
24
DANN
Benign
0.84
Eigen
Benign
-0.059
Eigen_PC
Benign
0.10
FATHMM_MKL
Pathogenic
0.98
D
LIST_S2
Uncertain
0.86
.;D
M_CAP
Benign
0.0072
T
MetaRNN
Benign
0.13
T;T
MetaSVM
Benign
-0.92
T
MutationTaster
Benign
1.0
D;D
PROVEAN
Benign
-0.36
N;N
REVEL
Benign
0.17
Sift
Benign
0.31
T;T
Sift4G
Benign
0.28
T;T
Vest4
0.32
MVP
0.28
MPC
0.20
ClinPred
0.11
T
GERP RS
6.1
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7
gMVP
0.51

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.090
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs776954576; hg19: chr10-104622652; API