10-58751999-T-G

Variant names:

• chr10-58751999-T-G
• rs10763586
• NM_001080512.3:c.308-33002T>G

Variant summary

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

The NM_001080512.3(BICC1):​c.308-33002T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.65 in 152,050 control chromosomes in the GnomAD database, including 32,860 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 0.65 (32860 hom., cov: 33)
• Consequence: BICC1 NM_001080512.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.80
• Publications: 4 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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.882 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BICC1	NM_001080512.3	c.308-33002T>G		intron_variant	Intron 3 of 20	ENST00000373886.8	NP_001073981.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BICC1	ENST00000373886.8	c.308-33002T>G		intron_variant	Intron 3 of 20	1	NM_001080512.3	ENSP00000362993.3

Frequencies

GnomAD3 genomes AF: 0.649 AC: 98668 AN: 151932 Hom.: 32820 Cov.: 33

Gnomad AFR AF: 0.512

Gnomad AMI AF: 0.774

Gnomad AMR AF: 0.733

Gnomad ASJ AF: 0.777

Gnomad EAS AF: 0.904

Gnomad SAS AF: 0.644

Gnomad FIN AF: 0.697

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.678

Gnomad OTH AF: 0.675

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

GnomAD4 genome AF: 0.650 AC: 98762 AN: 152050 Hom.: 32860 Cov.: 33 AF XY: 0.652 AC XY: 48433 AN XY: 74302

African (AFR) AF: 0.513 AC: 21275 AN: 41486

American (AMR) AF: 0.734 AC: 11200 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.777 AC: 2697 AN: 3472

East Asian (EAS) AF: 0.903 AC: 4672 AN: 5172

South Asian (SAS) AF: 0.645 AC: 3113 AN: 4824

European-Finnish (FIN) AF: 0.697 AC: 7349 AN: 10548

Middle Eastern (MID) AF: 0.741 AC: 218 AN: 294

European-Non Finnish (NFE) AF: 0.678 AC: 46104 AN: 67972

Other (OTH) AF: 0.678 AC: 1431 AN: 2110

Alfa AF: 0.673 Hom.: 5899

Bravo AF: 0.650

Asia WGS AF: 0.763 AC: 2652 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.12
DANN	Benign	0.54
PhyloP100		-1.8
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: rs10763586; hg19: chr10-60511759;