10-58820875-T-C

Variant names:

• chr10-58820875-T-C
• rs1899979
• NM_001080512.3:c.2794+407T>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.2794+407T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.718 in 152,002 control chromosomes in the GnomAD database, including 39,371 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 0.72 (39371 hom., cov: 33)
• Consequence: BICC1 NM_001080512.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.248
• Publications: 5 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

ENSG00000301981 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.737 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BICC1	NM_001080512.3	MANE Select	c.2794+407T>C		intron	N/A	NP_001073981.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BICC1	ENST00000373886.8	TSL:1 MANE Select	c.2794+407T>C		intron	N/A	ENSP00000362993.3
	ENSG00000301981	ENST00000783190.1		n.210-913A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.718 AC: 109125 AN: 151884 Hom.: 39349 Cov.: 33

Gnomad AFR AF: 0.670

Gnomad AMI AF: 0.733

Gnomad AMR AF: 0.747

Gnomad ASJ AF: 0.609

Gnomad EAS AF: 0.745

Gnomad SAS AF: 0.727

Gnomad FIN AF: 0.733

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.743

Gnomad OTH AF: 0.694

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

GnomAD4 genome AF: 0.718 AC: 109195 AN: 152002 Hom.: 39371 Cov.: 33 AF XY: 0.719 AC XY: 53369 AN XY: 74276

African (AFR) AF: 0.670 AC: 27796 AN: 41484

American (AMR) AF: 0.748 AC: 11400 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.609 AC: 2111 AN: 3468

East Asian (EAS) AF: 0.745 AC: 3836 AN: 5148

South Asian (SAS) AF: 0.726 AC: 3500 AN: 4818

European-Finnish (FIN) AF: 0.733 AC: 7752 AN: 10578

Middle Eastern (MID) AF: 0.694 AC: 204 AN: 294

European-Non Finnish (NFE) AF: 0.743 AC: 50470 AN: 67952

Other (OTH) AF: 0.694 AC: 1462 AN: 2106

Alfa AF: 0.726 Hom.: 51916

Bravo AF: 0.717

Asia WGS AF: 0.704 AC: 2447 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	5.3
DANN	Benign	0.82
PhyloP100		-0.25
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: rs1899979; hg19: chr10-60580635;