rs1658442

Variant names:

• chr10-58559137-G-A
• rs1658442
• NM_001080512.3:c.190+45804G>A

Your query was ambiguous. Multiple possible variants found:

• chr10-58559137-G-A
• chr10-58559137-G-C
• chr10-58559137-G-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+45804G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.435 in 151,452 control chromosomes in the GnomAD database, including 16,117 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 0.44 (16117 hom., cov: 31)
• Consequence: BICC1 NM_001080512.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0800
• Publications: 13 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.608 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BICC1	NM_001080512.3	c.190+45804G>A		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.190+45804G>A		intron_variant	Intron 1 of 20	1	NM_001080512.3	ENSP00000362993.3

Frequencies

GnomAD3 genomes AF: 0.435 AC: 65889 AN: 151332 Hom.: 16100 Cov.: 31

Gnomad AFR AF: 0.201

Gnomad AMI AF: 0.670

Gnomad AMR AF: 0.617

Gnomad ASJ AF: 0.497

Gnomad EAS AF: 0.521

Gnomad SAS AF: 0.451

Gnomad FIN AF: 0.453

Gnomad MID AF: 0.455

Gnomad NFE AF: 0.519

Gnomad OTH AF: 0.447

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

GnomAD4 genome AF: 0.435 AC: 65911 AN: 151452 Hom.: 16117 Cov.: 31 AF XY: 0.435 AC XY: 32213 AN XY: 73990

African (AFR) AF: 0.201 AC: 8294 AN: 41242

American (AMR) AF: 0.618 AC: 9388 AN: 15190

Ashkenazi Jewish (ASJ) AF: 0.497 AC: 1723 AN: 3464

East Asian (EAS) AF: 0.521 AC: 2670 AN: 5122

South Asian (SAS) AF: 0.452 AC: 2167 AN: 4798

European-Finnish (FIN) AF: 0.453 AC: 4751 AN: 10478

Middle Eastern (MID) AF: 0.452 AC: 132 AN: 292

European-Non Finnish (NFE) AF: 0.519 AC: 35244 AN: 67850

Other (OTH) AF: 0.443 AC: 934 AN: 2108

Alfa AF: 0.395 Hom.: 5143

Bravo AF: 0.443

Asia WGS AF: 0.427 AC: 1479 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.98
DANN	Benign	0.40
PhyloP100		0.080
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: rs1658442; hg19: chr10-60318897;