rs12264028

Positions:

• chr10-58518380-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001080512.3(BICC1):​c.190+5047C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.54 in 151,766 control chromosomes in the GnomAD database, including 23,205 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 0.54 (23205 hom., cov: 31)
• Consequence: BICC1 NM_001080512.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.49

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.704 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BICC1	NM_001080512.3	c.190+5047C>T		intron_variant		ENST00000373886.8	NP_001073981.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BICC1	ENST00000373886.8	c.190+5047C>T		intron_variant		1	NM_001080512.3	ENSP00000362993.3

Frequencies

GnomAD3 genomes AF: 0.540 AC: 81901 AN: 151648 Hom.: 23154 Cov.: 31

Gnomad AFR AF: 0.710

Gnomad AMI AF: 0.333

Gnomad AMR AF: 0.376

Gnomad ASJ AF: 0.504

Gnomad EAS AF: 0.480

Gnomad SAS AF: 0.546

Gnomad FIN AF: 0.549

Gnomad MID AF: 0.545

Gnomad NFE AF: 0.481

Gnomad OTH AF: 0.536

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

GnomAD4 genome AF: 0.540 AC: 81995 AN: 151766 Hom.: 23205 Cov.: 31 AF XY: 0.541 AC XY: 40101 AN XY: 74136

Gnomad4 AFR AF: 0.711

Gnomad4 AMR AF: 0.376

Gnomad4 ASJ AF: 0.504

Gnomad4 EAS AF: 0.479

Gnomad4 SAS AF: 0.546

Gnomad4 FIN AF: 0.549

Gnomad4 NFE AF: 0.481

Gnomad4 OTH AF: 0.540

Alfa AF: 0.519 Hom.: 3585

Bravo AF: 0.529

Asia WGS AF: 0.563 AC: 1957 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.036
DANN	Benign	0.59

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: rs12264028; hg19: chr10-60278140;