chr13-102839828-G-C

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_017693.4(BIVM):ā€‹c.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

Scores

1
17

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 4.67
Variant links:
Genes affected
BIVM (HGNC:16034): (basic, immunoglobulin-like variable motif containing) Located in extracellular space. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

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
BIVMNM_017693.4 linkuse as main transcriptc.1475G>C p.Gly492Ala missense_variant 11/11 ENST00000257336.6
BIVM-ERCC5NM_001204425.2 linkuse as main transcriptc.1450+25G>C intron_variant
BIVMNM_001159596.2 linkuse as main transcriptc.809G>C p.Gly270Ala missense_variant 9/9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
BIVMENST00000257336.6 linkuse as main transcriptc.1475G>C p.Gly492Ala missense_variant 11/111 NM_017693.4 P1Q86UB2-1

Frequencies

GnomAD3 genomes
AF:
0.000164
AC:
25
AN:
152132
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.000483
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000262
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.000478
GnomAD3 exomes
AF:
0.0000279
AC:
7
AN:
250710
Hom.:
0
AF XY:
0.0000221
AC XY:
3
AN XY:
135546
show subpopulations
Gnomad AFR exome
AF:
0.000431
Gnomad AMR exome
AF:
0.00
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:
0.0000185
AC:
27
AN:
1461218
Hom.:
0
Cov.:
31
AF XY:
0.0000151
AC XY:
11
AN XY:
726932
show subpopulations
Gnomad4 AFR exome
AF:
0.000747
Gnomad4 AMR exome
AF:
0.00
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:
8.99e-7
Gnomad4 OTH exome
AF:
0.0000166
GnomAD4 genome
AF:
0.000164
AC:
25
AN:
152250
Hom.:
0
Cov.:
32
AF XY:
0.000121
AC XY:
9
AN XY:
74432
show subpopulations
Gnomad4 AFR
AF:
0.000481
Gnomad4 AMR
AF:
0.000262
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.000473
Alfa
AF:
0.000142
Hom.:
0
Bravo
AF:
0.000223
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 GeneticsOct 26, 2022The 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: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.076
BayesDel_addAF
Benign
-0.37
T
BayesDel_noAF
Benign
-0.43
CADD
Benign
19
DANN
Benign
0.91
DEOGEN2
Benign
0.014
T;.
Eigen
Benign
-0.088
Eigen_PC
Benign
0.13
FATHMM_MKL
Pathogenic
0.97
D
LIST_S2
Benign
0.71
T;T
M_CAP
Benign
0.0042
T
MetaRNN
Benign
0.033
T;T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
-0.20
N;.
MutationTaster
Benign
1.0
D;D
PROVEAN
Benign
-0.68
N;N
REVEL
Benign
0.033
Sift
Benign
0.19
T;T
Sift4G
Benign
0.45
T;T
Polyphen
0.012
B;B
Vest4
0.18
MVP
0.14
MPC
0.30
ClinPred
0.056
T
GERP RS
4.5
Varity_R
0.090
gMVP
0.10

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
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: rs148535072; hg19: chr13-103492178; API