10-58527875-G-C

Position:

• chr10-58527875-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001080512.3(BICC1):​c.190+14542G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.46 in 151,716 control chromosomes in the GnomAD database, including 17,110 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 0.46 (17110 hom., cov: 31)
• Consequence: BICC1 NM_001080512.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.794

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.614 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BICC1	NM_001080512.3	c.190+14542G>C		intron_variant		ENST00000373886.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BICC1	ENST00000373886.8	c.190+14542G>C		intron_variant		1	NM_001080512.3	P1

Frequencies

GnomAD3 genomes AF: 0.460 AC: 69760 AN: 151598 Hom.: 17094 Cov.: 31

Gnomad AFR AF: 0.290

Gnomad AMI AF: 0.667

Gnomad AMR AF: 0.623

Gnomad ASJ AF: 0.496

Gnomad EAS AF: 0.520

Gnomad SAS AF: 0.454

Gnomad FIN AF: 0.453

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.519

Gnomad OTH AF: 0.463

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.460 AC: 69784 AN: 151716 Hom.: 17110 Cov.: 31 AF XY: 0.459 AC XY: 34051 AN XY: 74136

Gnomad4 AFR AF: 0.290

Gnomad4 AMR AF: 0.624

Gnomad4 ASJ AF: 0.496

Gnomad4 EAS AF: 0.521

Gnomad4 SAS AF: 0.454

Gnomad4 FIN AF: 0.453

Gnomad4 NFE AF: 0.519

Gnomad4 OTH AF: 0.459

Alfa AF: 0.336 Hom.: 886

Bravo AF: 0.471

Asia WGS AF: 0.436 AC: 1519 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.4
DANN	Benign	0.65

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: rs1346300; hg19: chr10-60287635;