3-52401896-G-A

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2

The NM_004656.4(BAP1):​c.*392C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00382 in 376,600 control chromosomes in the GnomAD database, including 22 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0079 ( 16 hom., cov: 33)
Exomes 𝑓: 0.0011 ( 6 hom. )

Consequence

BAP1
NM_004656.4 3_prime_UTR

Scores

8

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.709
Variant links:
Genes affected
BAP1 (HGNC:950): (BRCA1 associated protein 1) This gene belongs to the ubiquitin C-terminal hydrolase subfamily of deubiquitinating enzymes that are involved in the removal of ubiquitin from proteins. The encoded enzyme binds to the breast cancer type 1 susceptibility protein (BRCA1) via the RING finger domain of the latter and acts as a tumor suppressor. In addition, the enzyme may be involved in regulation of transcription, regulation of cell cycle and growth, response to DNA damage and chromatin dynamics. Germline mutations in this gene may be associated with tumor predisposition syndrome (TPDS), which involves increased risk of cancers including malignant mesothelioma, uveal melanoma and cutaneous melanoma. [provided by RefSeq, May 2013]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.006372899).
BP6
Variant 3-52401896-G-A is Benign according to our data. Variant chr3-52401896-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 903576.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00786 (1198/152360) while in subpopulation AFR AF= 0.0271 (1127/41576). AF 95% confidence interval is 0.0258. There are 16 homozygotes in gnomad4. There are 550 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
High AC in GnomAd4 at 1198 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
BAP1NM_004656.4 linkuse as main transcriptc.*392C>T 3_prime_UTR_variant 17/17 ENST00000460680.6 NP_004647.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
BAP1ENST00000460680.6 linkuse as main transcriptc.*392C>T 3_prime_UTR_variant 17/171 NM_004656.4 ENSP00000417132 P1

Frequencies

GnomAD3 genomes
AF:
0.00787
AC:
1198
AN:
152242
Hom.:
16
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0272
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00373
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00316
Gnomad NFE
AF:
0.0000735
Gnomad OTH
AF:
0.00383
GnomAD4 exome
AF:
0.00108
AC:
242
AN:
224240
Hom.:
6
Cov.:
0
AF XY:
0.000994
AC XY:
113
AN XY:
113714
show subpopulations
Gnomad4 AFR exome
AF:
0.0221
Gnomad4 AMR exome
AF:
0.00110
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000799
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000896
Gnomad4 OTH exome
AF:
0.00220
GnomAD4 genome
AF:
0.00786
AC:
1198
AN:
152360
Hom.:
16
Cov.:
33
AF XY:
0.00738
AC XY:
550
AN XY:
74498
show subpopulations
Gnomad4 AFR
AF:
0.0271
Gnomad4 AMR
AF:
0.00372
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000735
Gnomad4 OTH
AF:
0.00379
Alfa
AF:
0.00185
Hom.:
0
Bravo
AF:
0.00926
Asia WGS
AF:
0.00202
AC:
7
AN:
3478

ClinVar

Significance: Benign/Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

BAP1-related tumor predisposition syndrome Benign:1
Benign, criteria provided, single submitterclinical testingIllumina Laboratory Services, IlluminaJan 13, 2018This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
not provided Benign:1
Likely benign, criteria provided, single submitterclinical testingGeneDxJun 15, 2019- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
-0.74
T
BayesDel_noAF
Benign
-0.82
CADD
Benign
4.5
DANN
Benign
0.58
DEOGEN2
Benign
0.10
T
FATHMM_MKL
Benign
0.48
N
LIST_S2
Benign
0.38
T
MetaRNN
Benign
0.0064
T
MutationTaster
Benign
1.0
N;N
Vest4
0.18
MVP
0.73
GERP RS
1.3

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: rs112026686; hg19: chr3-52435912; API