rs1866168

Variant names:

• chr10-58601802-T-C
• rs1866168
• NM_001080512.3:c.191-19053T>C

Variant summary

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

The NM_001080512.3(BICC1):​c.191-19053T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.285 in 151,974 control chromosomes in the GnomAD database, including 6,485 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 0.29 (6485 hom., cov: 32)
• Consequence: BICC1 NM_001080512.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.224
• Publications: 2 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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.439 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BICC1	NM_001080512.3	c.191-19053T>C		intron_variant	Intron 1 of 20	ENST00000373886.8	NP_001073981.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BICC1	ENST00000373886.8	c.191-19053T>C		intron_variant	Intron 1 of 20	1	NM_001080512.3	ENSP00000362993.3

Frequencies

GnomAD3 genomes AF: 0.285 AC: 43273 AN: 151856 Hom.: 6464 Cov.: 32

Gnomad AFR AF: 0.291

Gnomad AMI AF: 0.120

Gnomad AMR AF: 0.192

Gnomad ASJ AF: 0.237

Gnomad EAS AF: 0.455

Gnomad SAS AF: 0.402

Gnomad FIN AF: 0.344

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.276

Gnomad OTH AF: 0.285

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

GnomAD4 genome AF: 0.285 AC: 43315 AN: 151974 Hom.: 6485 Cov.: 32 AF XY: 0.289 AC XY: 21448 AN XY: 74270

African (AFR) AF: 0.291 AC: 12093 AN: 41496

American (AMR) AF: 0.192 AC: 2929 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.237 AC: 821 AN: 3468

East Asian (EAS) AF: 0.454 AC: 2344 AN: 5162

South Asian (SAS) AF: 0.402 AC: 1939 AN: 4824

European-Finnish (FIN) AF: 0.344 AC: 3629 AN: 10544

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.276 AC: 18757 AN: 67896

Other (OTH) AF: 0.291 AC: 614 AN: 2110

Alfa AF: 0.283 Hom.: 3600

Bravo AF: 0.269

Asia WGS AF: 0.435 AC: 1499 AN: 3450

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.4
DANN	Benign	0.66
PhyloP100		0.22
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: rs1866168; hg19: chr10-60361562; COSMIC: COSV65866204;