chr10-58518380-C-T

Variant names:

• chr10-58518380-C-T
• rs12264028
• NM_001080512.3:c.190+5047C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001080512.3(BICC1):​c.190+5047C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.54 in 151,766 control chromosomes in the GnomAD database, including 23,205 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 0.54 (23205 hom., cov: 31)
• Consequence: BICC1 NM_001080512.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.49
• Publications: 8 publications found

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 Gene-Disease associations (from GenCC):

• renal dysplasia, cystic, susceptibility to

  Inheritance: AD, Unknown Classification: MODERATE, LIMITED Submitted by: Broad Center for Mendelian Genomics, Labcorp Genetics (formerly Invitae), Ambry Genetics

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.704 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001080512.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BICC1	NM_001080512.3	MANE Select	c.190+5047C>T		intron	N/A	NP_001073981.1	Q9H694-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BICC1	ENST00000373886.8	TSL:1 MANE Select	c.190+5047C>T		intron	N/A	ENSP00000362993.3	Q9H694-1

Frequencies

GnomAD3 genomes AF: 0.540 AC: 81901 AN: 151648 Hom.: 23154 Cov.: 31

Gnomad AFR AF: 0.710

Gnomad AMI AF: 0.333

Gnomad AMR AF: 0.376

Gnomad ASJ AF: 0.504

Gnomad EAS AF: 0.480

Gnomad SAS AF: 0.546

Gnomad FIN AF: 0.549

Gnomad MID AF: 0.545

Gnomad NFE AF: 0.481

Gnomad OTH AF: 0.536

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

GnomAD4 genome AF: 0.540 AC: 81995 AN: 151766 Hom.: 23205 Cov.: 31 AF XY: 0.541 AC XY: 40101 AN XY: 74136

African (AFR) AF: 0.711 AC: 29427 AN: 41406

American (AMR) AF: 0.376 AC: 5726 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.504 AC: 1748 AN: 3466

East Asian (EAS) AF: 0.479 AC: 2450 AN: 5112

South Asian (SAS) AF: 0.546 AC: 2621 AN: 4800

European-Finnish (FIN) AF: 0.549 AC: 5770 AN: 10508

Middle Eastern (MID) AF: 0.548 AC: 160 AN: 292

European-Non Finnish (NFE) AF: 0.481 AC: 32648 AN: 67912

Other (OTH) AF: 0.540 AC: 1142 AN: 2114

Alfa AF: 0.524 Hom.: 3775

Bravo AF: 0.529

Asia WGS AF: 0.563 AC: 1957 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.036
DANN	Benign	0.59
PhyloP100		-3.5
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs12264028; hg19: chr10-60278140;