NM_001080512.3:c.1180-522A>G

Variant names:

• chr10-58795818-A-G
• rs11006263
• NM_001080512.3:c.1180-522A>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.1180-522A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0654 in 152,218 control chromosomes in the GnomAD database, including 333 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 0.065 (333 hom., cov: 32)
• Consequence: BICC1 NM_001080512.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.760
• Publications: 6 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=-0.72).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0848 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BICC1	NM_001080512.3	c.1180-522A>G		intron_variant	Intron 9 of 20	ENST00000373886.8	NP_001073981.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BICC1	ENST00000373886.8	c.1180-522A>G		intron_variant	Intron 9 of 20	1	NM_001080512.3	ENSP00000362993.3
BICC1	ENST00000263103.1	c.58-522A>G		intron_variant	Intron 1 of 9	1		ENSP00000263103.1

Frequencies

GnomAD3 genomes AF: 0.0653 AC: 9927 AN: 152100 Hom.: 330 Cov.: 32

Gnomad AFR AF: 0.0869

Gnomad AMI AF: 0.0692

Gnomad AMR AF: 0.0393

Gnomad ASJ AF: 0.0490

Gnomad EAS AF: 0.0369

Gnomad SAS AF: 0.0618

Gnomad FIN AF: 0.0978

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0565

Gnomad OTH AF: 0.0512

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

GnomAD4 genome AF: 0.0654 AC: 9951 AN: 152218 Hom.: 333 Cov.: 32 AF XY: 0.0661 AC XY: 4923 AN XY: 74432

African (AFR) AF: 0.0872 AC: 3620 AN: 41528

American (AMR) AF: 0.0393 AC: 601 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0490 AC: 170 AN: 3470

East Asian (EAS) AF: 0.0370 AC: 192 AN: 5194

South Asian (SAS) AF: 0.0623 AC: 300 AN: 4818

European-Finnish (FIN) AF: 0.0978 AC: 1035 AN: 10588

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0565 AC: 3843 AN: 68006

Other (OTH) AF: 0.0521 AC: 110 AN: 2110

Alfa AF: 0.0575 Hom.: 723

Bravo AF: 0.0616

Asia WGS AF: 0.0550 AC: 192 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	0.0060
DANN	Benign	0.84
PhyloP100		-0.76
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: rs11006263; hg19: chr10-60555578;