9-113360674-A-G

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_017688.3(BSPRY):ā€‹c.468A>Gā€‹(p.Lys156=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.243 in 1,606,006 control chromosomes in the GnomAD database, including 52,617 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: š‘“ 0.31 ( 8344 hom., cov: 32)
Exomes š‘“: 0.24 ( 44273 hom. )

Consequence

BSPRY
NM_017688.3 synonymous

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.08
Variant links:
Genes affected
BSPRY (HGNC:18232): (B-box and SPRY domain containing) Predicted to enable ubiquitin protein ligase activity. Predicted to be involved in protein ubiquitination. Predicted to act upstream of or within cellular response to leukemia inhibitory factor. Predicted to be located in cell leading edge; membrane; and perinuclear region of cytoplasm. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.51).
BP7
Synonymous conserved (PhyloP=1.08 with no splicing effect.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.479 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
BSPRYNM_017688.3 linkuse as main transcriptc.468A>G p.Lys156= synonymous_variant 3/6 ENST00000374183.5
BSPRYNM_001317943.2 linkuse as main transcriptc.468A>G p.Lys156= synonymous_variant 3/6
BSPRYNM_001317944.2 linkuse as main transcriptc.468A>G p.Lys156= synonymous_variant 3/5
BSPRYXM_006717149.4 linkuse as main transcriptc.468A>G p.Lys156= synonymous_variant 3/6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
BSPRYENST00000374183.5 linkuse as main transcriptc.468A>G p.Lys156= synonymous_variant 3/61 NM_017688.3 P1Q5W0U4-1
BSPRYENST00000462085.1 linkuse as main transcriptn.506A>G non_coding_transcript_exon_variant 3/51

Frequencies

GnomAD3 genomes
AF:
0.305
AC:
46354
AN:
151932
Hom.:
8300
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.484
Gnomad AMI
AF:
0.281
Gnomad AMR
AF:
0.330
Gnomad ASJ
AF:
0.263
Gnomad EAS
AF:
0.398
Gnomad SAS
AF:
0.285
Gnomad FIN
AF:
0.119
Gnomad MID
AF:
0.297
Gnomad NFE
AF:
0.217
Gnomad OTH
AF:
0.309
GnomAD3 exomes
AF:
0.263
AC:
62259
AN:
237162
Hom.:
9302
AF XY:
0.256
AC XY:
32895
AN XY:
128736
show subpopulations
Gnomad AFR exome
AF:
0.489
Gnomad AMR exome
AF:
0.355
Gnomad ASJ exome
AF:
0.263
Gnomad EAS exome
AF:
0.397
Gnomad SAS exome
AF:
0.274
Gnomad FIN exome
AF:
0.118
Gnomad NFE exome
AF:
0.208
Gnomad OTH exome
AF:
0.253
GnomAD4 exome
AF:
0.236
AC:
343715
AN:
1453956
Hom.:
44273
Cov.:
35
AF XY:
0.237
AC XY:
171085
AN XY:
722652
show subpopulations
Gnomad4 AFR exome
AF:
0.499
Gnomad4 AMR exome
AF:
0.350
Gnomad4 ASJ exome
AF:
0.266
Gnomad4 EAS exome
AF:
0.444
Gnomad4 SAS exome
AF:
0.278
Gnomad4 FIN exome
AF:
0.118
Gnomad4 NFE exome
AF:
0.217
Gnomad4 OTH exome
AF:
0.265
GnomAD4 genome
AF:
0.306
AC:
46456
AN:
152050
Hom.:
8344
Cov.:
32
AF XY:
0.304
AC XY:
22570
AN XY:
74338
show subpopulations
Gnomad4 AFR
AF:
0.485
Gnomad4 AMR
AF:
0.329
Gnomad4 ASJ
AF:
0.263
Gnomad4 EAS
AF:
0.398
Gnomad4 SAS
AF:
0.285
Gnomad4 FIN
AF:
0.119
Gnomad4 NFE
AF:
0.217
Gnomad4 OTH
AF:
0.309
Alfa
AF:
0.243
Hom.:
9449
Bravo
AF:
0.328
Asia WGS
AF:
0.339
AC:
1178
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.51
CADD
Benign
12
DANN
Benign
0.62

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
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: rs752757; hg19: chr9-116122954; COSMIC: COSV65242599; API