10-58776160-T-C

Variant summary

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

The NM_001080512.3(BICC1):​c.308-8841T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.782 in 152,140 control chromosomes in the GnomAD database, including 46,974 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 0.78 ( 46974 hom., cov: 32)

Consequence

BICC1
NM_001080512.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.107
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=-0.83).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.973 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
BICC1NM_001080512.3 linkuse as main transcriptc.308-8841T>C 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.308-8841T>C intron_variant 1 NM_001080512.3 ENSP00000362993 P1Q9H694-1

Frequencies

GnomAD3 genomes
AF:
0.782
AC:
118863
AN:
152022
Hom.:
46945
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.675
Gnomad AMI
AF:
0.900
Gnomad AMR
AF:
0.866
Gnomad ASJ
AF:
0.878
Gnomad EAS
AF:
0.996
Gnomad SAS
AF:
0.847
Gnomad FIN
AF:
0.841
Gnomad MID
AF:
0.867
Gnomad NFE
AF:
0.790
Gnomad OTH
AF:
0.809
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.782
AC:
118935
AN:
152140
Hom.:
46974
Cov.:
32
AF XY:
0.786
AC XY:
58453
AN XY:
74380
show subpopulations
Gnomad4 AFR
AF:
0.675
Gnomad4 AMR
AF:
0.866
Gnomad4 ASJ
AF:
0.878
Gnomad4 EAS
AF:
0.996
Gnomad4 SAS
AF:
0.846
Gnomad4 FIN
AF:
0.841
Gnomad4 NFE
AF:
0.790
Gnomad4 OTH
AF:
0.811
Alfa
AF:
0.799
Hom.:
66827
Bravo
AF:
0.782
Asia WGS
AF:
0.924
AC:
3209
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.83
CADD
Benign
2.2
DANN
Benign
0.62

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: rs999845; hg19: chr10-60535920; API