10-58513429-ACGGC-A

Position:

• chr10-58513429-ACGGC-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_001080512.3(BICC1):​c.190+104_190+107del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.466 in 1,199,972 control chromosomes in the GnomAD database, including 135,737 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.51 (20095 hom., cov: 0)
  • Exomes 𝑓: 0.46 (115642 hom.)
• Consequence: BICC1 NM_001080512.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.413

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]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 10-58513429-ACGGC-A is Benign according to our data. Variant chr10-58513429-ACGGC-A is described in ClinVar as [Benign]. Clinvar id is 1275954.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.599 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BICC1	NM_001080512.3	c.190+104_190+107del		intron_variant		ENST00000373886.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BICC1	ENST00000373886.8	c.190+104_190+107del		intron_variant		1	NM_001080512.3	P1

Frequencies

GnomAD3 genomes AF: 0.509 AC: 77213 AN: 151674 Hom.: 20063 Cov.: 0

Gnomad AFR AF: 0.605

Gnomad AMI AF: 0.330

Gnomad AMR AF: 0.366

Gnomad ASJ AF: 0.503

Gnomad EAS AF: 0.462

Gnomad SAS AF: 0.561

Gnomad FIN AF: 0.546

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.480

Gnomad OTH AF: 0.514

GnomAD4 exome AF: 0.460 AC: 481846 AN: 1048180 Hom.: 115642 AF XY: 0.464 AC XY: 238475 AN XY: 514348

Gnomad4 AFR exome AF: 0.608

Gnomad4 AMR exome AF: 0.275

Gnomad4 ASJ exome AF: 0.493

Gnomad4 EAS exome AF: 0.487

Gnomad4 SAS exome AF: 0.566

Gnomad4 FIN exome AF: 0.544

Gnomad4 NFE exome AF: 0.446

Gnomad4 OTH exome AF: 0.475

GnomAD4 genome AF: 0.509 AC: 77288 AN: 151792 Hom.: 20095 Cov.: 0 AF XY: 0.511 AC XY: 37931 AN XY: 74192

Gnomad4 AFR AF: 0.605

Gnomad4 AMR AF: 0.365

Gnomad4 ASJ AF: 0.503

Gnomad4 EAS AF: 0.462

Gnomad4 SAS AF: 0.560

Gnomad4 FIN AF: 0.546

Gnomad4 NFE AF: 0.479

Gnomad4 OTH AF: 0.518

Alfa AF: 0.512 Hom.: 2440

Bravo AF: 0.493

Asia WGS AF: 0.556 AC: 1931 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 10, 2018

- -

Computational scores

Source: dbNSFP v4.3

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

Other links and lift over

dbSNP: rs10571555; hg19: chr10-60273189;