Variant chr10-58620793-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2

The NM_001080512.3(BICC1):c.191-62C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0409 in 1,525,238 control chromosomes in the GnomAD database, including 1,568 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.031 ( 125 hom., cov: 32)

Exomes 𝑓: 0.042 ( 1443 hom. )

Consequence

BICC1
NM_001080512.3 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -2.03

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=-0.97).

BP6

Variant 10-58620793-C-T is Benign according to our data. Variant chr10-58620793-C-T is described in ClinVar as [Benign]. Clinvar id is 1247029.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.031 (4717/152112) while in subpopulation NFE AF= 0.0462 (3145/68012). AF 95% confidence interval is 0.0449. There are 125 homozygotes in gnomad4. There are 2290 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High AC in GnomAd4 at 4717 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BICC1	NM_001080512.3 linkuse as main transcript	c.191-62C>T		intron_variant		ENST00000373886.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BICC1	ENST00000373886.8 linkuse as main transcript	c.191-62C>T		intron_variant		1	NM_001080512.3	P1	Q9H694-1

Frequencies

GnomAD3 genomes

AF:

0.0310

AC:

4716

AN:

151994

Hom.:

125

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00720

Gnomad AMI

AF:

0.0208

Gnomad AMR

AF:

0.0219

Gnomad ASJ

AF:

0.0150

Gnomad EAS

AF:

0.000385

Gnomad SAS

AF:

0.00520

Gnomad FIN

AF:

0.0742

Gnomad MID

AF:

0.00637

Gnomad NFE

AF:

0.0462

Gnomad OTH

AF:

0.0273

GnomAD4 exome

AF:

0.0420

AC:

57699

AN:

1373126

Hom.:

1443

AF XY:

0.0410

AC XY:

28165

AN XY:

686606

show subpopulations

Gnomad4 AFR exome

AF:

0.00665

Gnomad4 AMR exome

AF:

0.0128

Gnomad4 ASJ exome

AF:

0.0169

Gnomad4 EAS exome

AF:

0.000129

Gnomad4 SAS exome

AF:

0.00704

Gnomad4 FIN exome

AF:

0.0775

Gnomad4 NFE exome

AF:

0.0480

Gnomad4 OTH exome

AF:

0.0346

GnomAD4 genome

AF:

0.0310

AC:

4717

AN:

152112

Hom.:

125

Cov.:

AF XY:

0.0308

AC XY:

2290

AN XY:

74332

show subpopulations

Gnomad4 AFR

AF:

0.00718

Gnomad4 AMR

AF:

0.0219

Gnomad4 ASJ

AF:

0.0150

Gnomad4 EAS

AF:

0.000386

Gnomad4 SAS

AF:

0.00541

Gnomad4 FIN

AF:

0.0742

Gnomad4 NFE

AF:

0.0462

Gnomad4 OTH

AF:

0.0275

Alfa

AF:

0.0407

Hom.:

Bravo

AF:

0.0264

Asia WGS

AF:

0.00520

AC:

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	clinical testing	GeneDx	Sep 06, 2019	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

0.0050

DANN

Benign

0.36

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