rs12264028

Variant summary

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

The ENST00000373886.8(BICC1):​c.190+5047C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.54 in 151,766 control chromosomes in the GnomAD database, including 23,205 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 0.54 ( 23205 hom., cov: 31)

Consequence

BICC1
ENST00000373886.8 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.49
Variant links:
Genes affected
BICC1 (HGNC:19351): (BicC family RNA binding protein 1) This gene encodes an RNA-binding protein that is active in regulating gene expression by modulating protein translation during embryonic development. Mouse studies identified the corresponding protein to be under strict control during cell differentiation and to be a maternally provided gene product. [provided by RefSeq, Apr 2009]

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=-0.91).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.704 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
BICC1NM_001080512.3 linkuse as main transcriptc.190+5047C>T intron_variant ENST00000373886.8 NP_001073981.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
BICC1ENST00000373886.8 linkuse as main transcriptc.190+5047C>T intron_variant 1 NM_001080512.3 ENSP00000362993 P1Q9H694-1

Frequencies

GnomAD3 genomes
AF:
0.540
AC:
81901
AN:
151648
Hom.:
23154
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.710
Gnomad AMI
AF:
0.333
Gnomad AMR
AF:
0.376
Gnomad ASJ
AF:
0.504
Gnomad EAS
AF:
0.480
Gnomad SAS
AF:
0.546
Gnomad FIN
AF:
0.549
Gnomad MID
AF:
0.545
Gnomad NFE
AF:
0.481
Gnomad OTH
AF:
0.536
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.540
AC:
81995
AN:
151766
Hom.:
23205
Cov.:
31
AF XY:
0.541
AC XY:
40101
AN XY:
74136
show subpopulations
Gnomad4 AFR
AF:
0.711
Gnomad4 AMR
AF:
0.376
Gnomad4 ASJ
AF:
0.504
Gnomad4 EAS
AF:
0.479
Gnomad4 SAS
AF:
0.546
Gnomad4 FIN
AF:
0.549
Gnomad4 NFE
AF:
0.481
Gnomad4 OTH
AF:
0.540
Alfa
AF:
0.519
Hom.:
3585
Bravo
AF:
0.529
Asia WGS
AF:
0.563
AC:
1957
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
0.036
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: rs12264028; hg19: chr10-60278140; API