chr13-102839828-G-C
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Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_017693.4(BIVM):āc.1475G>Cā(p.Gly492Ala) variant causes a missense change. The variant allele was found at a frequency of 0.0000322 in 1,613,468 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Genomes: š 0.00016 ( 0 hom., cov: 32)
Exomes š: 0.000018 ( 0 hom. )
Consequence
BIVM
NM_017693.4 missense
NM_017693.4 missense
Scores
1
17
Clinical Significance
Conservation
PhyloP100: 4.67
Genes affected
BIVM (HGNC:16034): (basic, immunoglobulin-like variable motif containing) Located in extracellular space. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.03322661).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BIVM | NM_017693.4 | c.1475G>C | p.Gly492Ala | missense_variant | 11/11 | ENST00000257336.6 | |
BIVM-ERCC5 | NM_001204425.2 | c.1450+25G>C | intron_variant | ||||
BIVM | NM_001159596.2 | c.809G>C | p.Gly270Ala | missense_variant | 9/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BIVM | ENST00000257336.6 | c.1475G>C | p.Gly492Ala | missense_variant | 11/11 | 1 | NM_017693.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000164 AC: 25AN: 152132Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000279 AC: 7AN: 250710Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135546
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GnomAD4 exome AF: 0.0000185 AC: 27AN: 1461218Hom.: 0 Cov.: 31 AF XY: 0.0000151 AC XY: 11AN XY: 726932
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GnomAD4 genome AF: 0.000164 AC: 25AN: 152250Hom.: 0 Cov.: 32 AF XY: 0.000121 AC XY: 9AN XY: 74432
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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 submitter | clinical testing | Ambry Genetics | Oct 26, 2022 | The c.1475G>C (p.G492A) alteration is located in exon 11 (coding exon 9) of the BIVM gene. This alteration results from a G to C substitution at nucleotide position 1475, causing the glycine (G) at amino acid position 492 to be replaced by an alanine (A). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
DEOGEN2
Benign
T;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Pathogenic
D
LIST_S2
Benign
T;T
M_CAP
Benign
T
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationAssessor
Benign
N;.
MutationTaster
Benign
D;D
PROVEAN
Benign
N;N
REVEL
Benign
Sift
Benign
T;T
Sift4G
Benign
T;T
Polyphen
B;B
Vest4
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
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