rs11006267

chr10-58803874-A-Gchr10-58803874-A-T

Variant summary

Our verdict is Benign. Variant got -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

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]

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BICC1	NM_001080512.3	c.2181+632A>G		intron_variant		ENST00000373886.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BICC1	ENST00000373886.8	c.2181+632A>G		intron_variant		1	NM_001080512.3	P1
BICC1	ENST00000263103.1	c.1059+632A>G		intron_variant		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

Gnomad4 AFR AF: 0.0112

Gnomad4 AMR AF: 0.0410

Gnomad4 ASJ AF: 0.0239

Gnomad4 EAS AF: 0.105

Gnomad4 SAS AF: 0.121

Gnomad4 FIN AF: 0.117

Gnomad4 NFE AF: 0.0574

Gnomad4 OTH AF: 0.0572

Alfa AF: 0.0508 Hom.: 112

Bravo AF: 0.0419

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	0.68
Dann	Benign	0.49

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

Publications

LitVar

Other links and lift over

dbSNP: rs11006267; hg19: chr10-60563634;