3-49641218-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_003458.4(BSN):​c.634-1050A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.281 in 152,008 control chromosomes in the GnomAD database, including 6,479 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: 𝑓 0.28 ( 6479 hom., cov: 32)

Consequence

BSN
NM_003458.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.318
Variant links:
Genes affected
BSN (HGNC:1117): (bassoon presynaptic cytomatrix protein) Neurotransmitters are released from a specific site in the axon terminal called the active zone, which is composed of synaptic vesicles and a meshwork of cytoskeleton underlying the plasma membrane. The protein encoded by this gene is thought to be a scaffolding protein involved in organizing the presynaptic cytoskeleton. The gene is expressed primarily in neurons in the brain. A similar gene product in rodents is concentrated in the active zone of axon terminals and tightly associated with cytoskeletal structures, and is essential for regulating neurotransmitter release from a subset of synapses. [provided by RefSeq, Jul 2008]
BSN-AS1 (HGNC:40102): (BSN antisense RNA 1)

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.288 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
BSNNM_003458.4 linkc.634-1050A>G intron_variant Intron 2 of 11 ENST00000296452.5 NP_003449.2 Q9UPA5

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
BSNENST00000296452.5 linkc.634-1050A>G intron_variant Intron 2 of 11 1 NM_003458.4 ENSP00000296452.4 Q9UPA5
BSN-AS1ENST00000442384.1 linkn.150+402T>C intron_variant Intron 1 of 1 3

Frequencies

GnomAD3 genomes
AF:
0.281
AC:
42668
AN:
151890
Hom.:
6475
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.272
Gnomad AMI
AF:
0.198
Gnomad AMR
AF:
0.209
Gnomad ASJ
AF:
0.443
Gnomad EAS
AF:
0.0455
Gnomad SAS
AF:
0.216
Gnomad FIN
AF:
0.448
Gnomad MID
AF:
0.320
Gnomad NFE
AF:
0.291
Gnomad OTH
AF:
0.288
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.281
AC:
42697
AN:
152008
Hom.:
6479
Cov.:
32
AF XY:
0.283
AC XY:
21005
AN XY:
74298
show subpopulations
Gnomad4 AFR
AF:
0.273
Gnomad4 AMR
AF:
0.208
Gnomad4 ASJ
AF:
0.443
Gnomad4 EAS
AF:
0.0456
Gnomad4 SAS
AF:
0.217
Gnomad4 FIN
AF:
0.448
Gnomad4 NFE
AF:
0.291
Gnomad4 OTH
AF:
0.286
Alfa
AF:
0.287
Hom.:
6401
Bravo
AF:
0.262
Asia WGS
AF:
0.135
AC:
475
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.84
CADD
Benign
7.6
DANN
Benign
0.59

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: rs4283605; hg19: chr3-49678651; API