10-58622734-G-C

Variant names:

• chr10-58622734-G-C
• rs10740740
• NM_001080512.3:c.237+1833G>C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_001080512.3(BICC1):​c.237+1833G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.61 in 151,956 control chromosomes in the GnomAD database, including 28,605 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 0.61 (28605 hom., cov: 33)
• Consequence: BICC1 NM_001080512.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.29
• 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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.24).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.666 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BICC1	NM_001080512.3	c.237+1833G>C		intron_variant	Intron 2 of 20	ENST00000373886.8	NP_001073981.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BICC1	ENST00000373886.8	c.237+1833G>C		intron_variant	Intron 2 of 20	1	NM_001080512.3	ENSP00000362993.3
BICC1	ENST00000476684.1	n.53+1833G>C		intron_variant	Intron 1 of 1	5

Frequencies

GnomAD3 genomes AF: 0.610 AC: 92672 AN: 151838 Hom.: 28577 Cov.: 33

Gnomad AFR AF: 0.673

Gnomad AMI AF: 0.411

Gnomad AMR AF: 0.651

Gnomad ASJ AF: 0.609

Gnomad EAS AF: 0.528

Gnomad SAS AF: 0.644

Gnomad FIN AF: 0.533

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.582

Gnomad OTH AF: 0.615

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

GnomAD4 genome AF: 0.610 AC: 92750 AN: 151956 Hom.: 28605 Cov.: 33 AF XY: 0.608 AC XY: 45172 AN XY: 74284

African (AFR) AF: 0.672 AC: 27870 AN: 41448

American (AMR) AF: 0.651 AC: 9943 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.609 AC: 2116 AN: 3472

East Asian (EAS) AF: 0.529 AC: 2722 AN: 5148

South Asian (SAS) AF: 0.644 AC: 3103 AN: 4822

European-Finnish (FIN) AF: 0.533 AC: 5621 AN: 10554

Middle Eastern (MID) AF: 0.592 AC: 174 AN: 294

European-Non Finnish (NFE) AF: 0.582 AC: 39524 AN: 67934

Other (OTH) AF: 0.618 AC: 1303 AN: 2110

Alfa AF: 0.461 Hom.: 1155

Bravo AF: 0.619

Asia WGS AF: 0.633 AC: 2199 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.24
CADD	Benign	16
DANN	Benign	0.80
PhyloP100		1.3
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: rs10740740; hg19: chr10-60382494;