Variant 10-58513361-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.190+28T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.478 in 1,555,464 control chromosomes in the GnomAD database, including 180,619 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.51 ( 20243 hom., cov: 33)

Exomes 𝑓: 0.47 ( 160376 hom. )

Consequence

BICC1
NM_001080512.3 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.570

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 (BayesDel_noAF=-0.84).

BP6

Variant 10-58513361-T-C is Benign according to our data. Variant chr10-58513361-T-C is described in ClinVar as [Benign]. Clinvar id is 1280720.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.6 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BICC1	NM_001080512.3 linkuse as main transcript	c.190+28T>C		intron_variant		ENST00000373886.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BICC1	ENST00000373886.8 linkuse as main transcript	c.190+28T>C		intron_variant		1	NM_001080512.3	P1	Q9H694-1

Frequencies

GnomAD3 genomes

AF:

0.510

AC:

77485

AN:

151904

Hom.:

20211

Cov.:

show subpopulations

Gnomad AFR

AF:

0.606

Gnomad AMI

AF:

0.333

Gnomad AMR

AF:

0.367

Gnomad ASJ

AF:

0.503

Gnomad EAS

AF:

0.462

Gnomad SAS

AF:

0.561

Gnomad FIN

AF:

0.548

Gnomad MID

AF:

0.544

Gnomad NFE

AF:

0.480

Gnomad OTH

AF:

0.514

GnomAD3 exomes

AF:

0.480

AC:

101793

AN:

212114

Hom.:

25355

AF XY:

0.489

AC XY:

56843

AN XY:

116152

show subpopulations

Gnomad AFR exome

AF:

0.619

Gnomad AMR exome

AF:

0.274

Gnomad ASJ exome

AF:

0.522

Gnomad EAS exome

AF:

0.466

Gnomad SAS exome

AF:

0.578

Gnomad FIN exome

AF:

0.552

Gnomad NFE exome

AF:

0.478

Gnomad OTH exome

AF:

0.451

GnomAD4 exome

AF:

0.475

AC:

666073

AN:

1403442

Hom.:

160376

Cov.:

AF XY:

0.479

AC XY:

332790

AN XY:

694872

show subpopulations

Gnomad4 AFR exome

AF:

0.624

Gnomad4 AMR exome

AF:

0.289

Gnomad4 ASJ exome

AF:

0.506

Gnomad4 EAS exome

AF:

0.490

Gnomad4 SAS exome

AF:

0.578

Gnomad4 FIN exome

AF:

0.550

Gnomad4 NFE exome

AF:

0.464

Gnomad4 OTH exome

AF:

0.488

GnomAD4 genome

AF:

0.510

AC:

77560

AN:

152022

Hom.:

20243

Cov.:

AF XY:

0.512

AC XY:

38073

AN XY:

74296

show subpopulations

Gnomad4 AFR

AF:

0.606

Gnomad4 AMR

AF:

0.366

Gnomad4 ASJ

AF:

0.503

Gnomad4 EAS

AF:

0.462

Gnomad4 SAS

AF:

0.561

Gnomad4 FIN

AF:

0.548

Gnomad4 NFE

AF:

0.480

Gnomad4 OTH

AF:

0.518

Alfa

AF:

0.492

Hom.:

4947

Bravo

AF:

0.493

Asia WGS

AF:

0.558

AC:

1939

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 10, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

3.5

DANN

Benign

0.31

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