Variant 10-58828793-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001080512.3(BICC1):c.2827T>C(p.Ser943Pro) variant causes a missense change. The variant allele was found at a frequency of 0.713 in 1,613,224 control chromosomes in the GnomAD database, including 414,483 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.64 ( 32750 hom., cov: 31)

Exomes 𝑓: 0.72 ( 381733 hom. )

Consequence

BICC1
NM_001080512.3 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 3.61

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]

BICC1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=1.4399488E-6).

BP6

Variant 10-58828793-T-C is Benign according to our data. Variant chr10-58828793-T-C is described in ClinVar as [Benign]. Clinvar id is 1297297.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.729 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BICC1	NM_001080512.3 linkuse as main transcript	c.2827T>C	p.Ser943Pro	missense_variant	21/21	ENST00000373886.8	NP_001073981.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BICC1	ENST00000373886.8 linkuse as main transcript	c.2827T>C	p.Ser943Pro	missense_variant	21/21	1	NM_001080512.3	ENSP00000362993	P1	Q9H694-1

Frequencies

GnomAD3 genomes

AF:

0.642

AC:

97494

AN:

151902

Hom.:

32745

Cov.:

show subpopulations

Gnomad AFR

AF:

0.429

Gnomad AMI

AF:

0.732

Gnomad AMR

AF:

0.717

Gnomad ASJ

AF:

0.605

Gnomad EAS

AF:

0.733

Gnomad SAS

AF:

0.670

Gnomad FIN

AF:

0.721

Gnomad MID

AF:

0.658

Gnomad NFE

AF:

0.734

Gnomad OTH

AF:

0.633

GnomAD3 exomes

AF:

0.707

AC:

176621

AN:

249830

Hom.:

63471

AF XY:

0.708

AC XY:

95708

AN XY:

135120

show subpopulations

Gnomad AFR exome

AF:

0.427

Gnomad AMR exome

AF:

0.788

Gnomad ASJ exome

AF:

0.620

Gnomad EAS exome

AF:

0.743

Gnomad SAS exome

AF:

0.672

Gnomad FIN exome

AF:

0.721

Gnomad NFE exome

AF:

0.731

Gnomad OTH exome

AF:

0.709

GnomAD4 exome

AF:

0.720

AC:

1052577

AN:

1461204

Hom.:

381733

Cov.:

AF XY:

0.720

AC XY:

523615

AN XY:

726928

show subpopulations

Gnomad4 AFR exome

AF:

0.422

Gnomad4 AMR exome

AF:

0.780

Gnomad4 ASJ exome

AF:

0.621

Gnomad4 EAS exome

AF:

0.733

Gnomad4 SAS exome

AF:

0.681

Gnomad4 FIN exome

AF:

0.727

Gnomad4 NFE exome

AF:

0.733

Gnomad4 OTH exome

AF:

0.697

GnomAD4 genome

AF:

0.642

AC:

97523

AN:

152020

Hom.:

32750

Cov.:

AF XY:

0.643

AC XY:

47800

AN XY:

74284

show subpopulations

Gnomad4 AFR

AF:

0.428

Gnomad4 AMR

AF:

0.718

Gnomad4 ASJ

AF:

0.605

Gnomad4 EAS

AF:

0.733

Gnomad4 SAS

AF:

0.669

Gnomad4 FIN

AF:

0.721

Gnomad4 NFE

AF:

0.734

Gnomad4 OTH

AF:

0.634

Alfa

AF:

0.709

Hom.:

97060

Bravo

AF:

0.632

TwinsUK

AF:

0.712

AC:

2640

ALSPAC

AF:

0.724

AC:

2791

ESP6500AA

AF:

0.441

AC:

1943

ESP6500EA

AF:

0.712

AC:

6127

ExAC

AF:

0.700

AC:

84966

Asia WGS

AF:

0.629

AC:

2188

AN:

3478

EpiCase

AF:

0.720

EpiControl

AF:

0.717

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 10, 2018	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 31, 2024	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.047

BayesDel_addAF

Benign

-0.76

BayesDel_noAF

Benign

-0.72

CADD

Benign

DANN

Benign

0.36

DEOGEN2

Benign

0.046

Eigen

Benign

-0.46

Eigen_PC

Benign

-0.21

FATHMM_MKL

Benign

0.27

LIST_S2

Benign

0.65

MetaRNN

Benign

0.0000014

MetaSVM

Benign

-1.0

MutationAssessor

Benign

-0.81

MutationTaster

Benign

0.86

PrimateAI

Benign

0.43

PROVEAN

Benign

-0.74

REVEL

Benign

0.12

Sift

Benign

1.0

Sift4G

Benign

0.22

Polyphen

0.0

Vest4

0.021

MPC

0.27

ClinPred

0.0071

GERP RS

3.9

Varity_R

0.13

gMVP

0.46

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over