rs682748

Variant summary

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

The NR_027253.1(BASP1-AS1):​n.1443+13667T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.512 in 151,982 control chromosomes in the GnomAD database, including 20,630 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 0.51 ( 20630 hom., cov: 32)

Consequence

BASP1-AS1
NR_027253.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.06
Variant links:
Genes affected
BASP1-AS1 (HGNC:26609): (BASP1 antisense RNA 1)
BASP1 (HGNC:957): (brain abundant membrane attached signal protein 1) This gene encodes a membrane bound protein with several transient phosphorylation sites and PEST motifs. Conservation of proteins with PEST sequences among different species supports their functional significance. PEST sequences typically occur in proteins with high turnover rates. Immunological characteristics of this protein are species specific. This protein also undergoes N-terminal myristoylation. Alternative splicing results in multiple transcript variants that encode the same protein. [provided by RefSeq, Oct 2012]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.97).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.594 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
BASP1-AS1NR_027253.1 linkuse as main transcriptn.1443+13667T>C intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
BASP1-AS1ENST00000655365.1 linkuse as main transcriptn.818+13667T>C intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.512
AC:
77793
AN:
151864
Hom.:
20615
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.387
Gnomad AMI
AF:
0.576
Gnomad AMR
AF:
0.604
Gnomad ASJ
AF:
0.524
Gnomad EAS
AF:
0.409
Gnomad SAS
AF:
0.468
Gnomad FIN
AF:
0.595
Gnomad MID
AF:
0.544
Gnomad NFE
AF:
0.564
Gnomad OTH
AF:
0.526
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.512
AC:
77848
AN:
151982
Hom.:
20630
Cov.:
32
AF XY:
0.513
AC XY:
38125
AN XY:
74312
show subpopulations
Gnomad4 AFR
AF:
0.387
Gnomad4 AMR
AF:
0.605
Gnomad4 ASJ
AF:
0.524
Gnomad4 EAS
AF:
0.409
Gnomad4 SAS
AF:
0.469
Gnomad4 FIN
AF:
0.595
Gnomad4 NFE
AF:
0.564
Gnomad4 OTH
AF:
0.523
Alfa
AF:
0.547
Hom.:
32168
Bravo
AF:
0.510
Asia WGS
AF:
0.418
AC:
1450
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.97
CADD
Benign
0.32
DANN
Benign
0.44

Splicing

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: rs682748; hg19: chr5-17148911; API