NM_001080512.3:c.2181+632A>G

Variant names:

• chr10-58803874-A-G
• rs11006267
• NM_001080512.3:c.2181+632A>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.2181+632A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0498 in 152,330 control chromosomes in the GnomAD database, including 276 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 0.050 (276 hom., cov: 33)
• Consequence: BICC1 NM_001080512.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.127
• 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=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.113 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.2181+632A>G		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.2181+632A>G		intron	N/A	ENSP00000362993.3
	BICC1	ENST00000263103.1	TSL:1	c.1059+632A>G		intron	N/A	ENSP00000263103.1

Frequencies

GnomAD3 genomes AF: 0.0499 AC: 7591 AN: 152212 Hom.: 274 Cov.: 33

Gnomad AFR AF: 0.0112

Gnomad AMI AF: 0.00989

Gnomad AMR AF: 0.0410

Gnomad ASJ AF: 0.0239

Gnomad EAS AF: 0.105

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0574

Gnomad OTH AF: 0.0568

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

GnomAD4 genome AF: 0.0498 AC: 7590 AN: 152330 Hom.: 276 Cov.: 33 AF XY: 0.0536 AC XY: 3990 AN XY: 74486

African (AFR) AF: 0.0112 AC: 465 AN: 41586

American (AMR) AF: 0.0410 AC: 628 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0239 AC: 83 AN: 3472

East Asian (EAS) AF: 0.105 AC: 546 AN: 5182

South Asian (SAS) AF: 0.121 AC: 583 AN: 4832

European-Finnish (FIN) AF: 0.117 AC: 1245 AN: 10608

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.0574 AC: 3906 AN: 68026

Other (OTH) AF: 0.0572 AC: 121 AN: 2116

Alfa AF: 0.0540 Hom.: 159

Bravo AF: 0.0419

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.68
DANN	Benign	0.49
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: rs11006267; hg19: chr10-60563634;