rs12571250

Variant names:

• chr10-58525859-G-A
• rs12571250
• NM_001080512.3:c.190+12526G>A

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+12526G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0335 in 151,624 control chromosomes in the GnomAD database, including 169 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 0.033 (169 hom., cov: 32)
• Consequence: BICC1 NM_001080512.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.127
• Publications: 1 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 (EAS) allele frequency at 95% confidence interval = 0.152 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BICC1	NM_001080512.3	c.190+12526G>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+12526G>A		intron_variant	Intron 1 of 20	1	NM_001080512.3	ENSP00000362993.3

Frequencies

GnomAD3 genomes AF: 0.0335 AC: 5074 AN: 151506 Hom.: 168 Cov.: 32

Gnomad AFR AF: 0.00690

Gnomad AMI AF: 0.0351

Gnomad AMR AF: 0.0213

Gnomad ASJ AF: 0.00953

Gnomad EAS AF: 0.161

Gnomad SAS AF: 0.0938

Gnomad FIN AF: 0.0744

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0334

Gnomad OTH AF: 0.0303

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

GnomAD4 genome AF: 0.0335 AC: 5075 AN: 151624 Hom.: 169 Cov.: 32 AF XY: 0.0369 AC XY: 2737 AN XY: 74122

African (AFR) AF: 0.00688 AC: 283 AN: 41128

American (AMR) AF: 0.0212 AC: 323 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.00953 AC: 33 AN: 3464

East Asian (EAS) AF: 0.161 AC: 827 AN: 5134

South Asian (SAS) AF: 0.0944 AC: 456 AN: 4828

European-Finnish (FIN) AF: 0.0744 AC: 787 AN: 10580

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 292

European-Non Finnish (NFE) AF: 0.0334 AC: 2268 AN: 67950

Other (OTH) AF: 0.0314 AC: 66 AN: 2104

Alfa AF: 0.0326 Hom.: 42

Bravo AF: 0.0270

Asia WGS AF: 0.124 AC: 430 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.2
DANN	Benign	0.58
PhyloP100		0.13
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: rs12571250; hg19: chr10-60285619;