10-58751999-T-G

Variant summary

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

The NM_001080512.3(BICC1):​c.308-33002T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.65 in 152,050 control chromosomes in the GnomAD database, including 32,860 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 0.65 ( 32860 hom., cov: 33)

Consequence

BICC1
NM_001080512.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.80
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=-0.97).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.882 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
BICC1NM_001080512.3 linkc.308-33002T>G intron_variant ENST00000373886.8 NP_001073981.1 Q9H694-1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
BICC1ENST00000373886.8 linkc.308-33002T>G intron_variant 1 NM_001080512.3 ENSP00000362993.3 Q9H694-1

Frequencies

GnomAD3 genomes
AF:
0.649
AC:
98668
AN:
151932
Hom.:
32820
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.512
Gnomad AMI
AF:
0.774
Gnomad AMR
AF:
0.733
Gnomad ASJ
AF:
0.777
Gnomad EAS
AF:
0.904
Gnomad SAS
AF:
0.644
Gnomad FIN
AF:
0.697
Gnomad MID
AF:
0.734
Gnomad NFE
AF:
0.678
Gnomad OTH
AF:
0.675
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.650
AC:
98762
AN:
152050
Hom.:
32860
Cov.:
33
AF XY:
0.652
AC XY:
48433
AN XY:
74302
show subpopulations
Gnomad4 AFR
AF:
0.513
Gnomad4 AMR
AF:
0.734
Gnomad4 ASJ
AF:
0.777
Gnomad4 EAS
AF:
0.903
Gnomad4 SAS
AF:
0.645
Gnomad4 FIN
AF:
0.697
Gnomad4 NFE
AF:
0.678
Gnomad4 OTH
AF:
0.678
Alfa
AF:
0.673
Hom.:
5899
Bravo
AF:
0.650
Asia WGS
AF:
0.763
AC:
2652
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
0.12
DANN
Benign
0.54

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: rs10763586; hg19: chr10-60511759; API