rs1649053

Positions:

• chr10-58561727-T-C

Variant summary

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

The ENST00000373886.8(BICC1):​c.190+48394T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.312 in 151,946 control chromosomes in the GnomAD database, including 9,246 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 0.31 (9246 hom., cov: 32)
• Consequence: BICC1 ENST00000373886.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.147

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=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.462 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BICC1	NM_001080512.3	c.190+48394T>C		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+48394T>C		intron_variant		1	NM_001080512.3	ENSP00000362993	P1

Frequencies

GnomAD3 genomes AF: 0.313 AC: 47470 AN: 151828 Hom.: 9239 Cov.: 32

Gnomad AFR AF: 0.0803

Gnomad AMI AF: 0.509

Gnomad AMR AF: 0.471

Gnomad ASJ AF: 0.421

Gnomad EAS AF: 0.233

Gnomad SAS AF: 0.283

Gnomad FIN AF: 0.369

Gnomad MID AF: 0.363

Gnomad NFE AF: 0.409

Gnomad OTH AF: 0.340

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

GnomAD4 genome AF: 0.312 AC: 47476 AN: 151946 Hom.: 9246 Cov.: 32 AF XY: 0.312 AC XY: 23196 AN XY: 74258

Gnomad4 AFR AF: 0.0801

Gnomad4 AMR AF: 0.471

Gnomad4 ASJ AF: 0.421

Gnomad4 EAS AF: 0.233

Gnomad4 SAS AF: 0.283

Gnomad4 FIN AF: 0.369

Gnomad4 NFE AF: 0.409

Gnomad4 OTH AF: 0.336

Alfa AF: 0.376 Hom.: 5442

Bravo AF: 0.314

Asia WGS AF: 0.237 AC: 825 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	4.2
DANN	Benign	0.75

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: rs1649053; hg19: chr10-60321487;