10-58820875-T-C

Position:

• chr10-58820875-T-C

Variant summary

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

The NM_001080512.3(BICC1):​c.2794+407T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.718 in 152,002 control chromosomes in the GnomAD database, including 39,371 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 0.72 (39371 hom., cov: 33)
• Consequence: BICC1 NM_001080512.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.248

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=-0.78).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.737 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BICC1	NM_001080512.3	c.2794+407T>C		intron_variant		ENST00000373886.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BICC1	ENST00000373886.8	c.2794+407T>C		intron_variant		1	NM_001080512.3	P1

Frequencies

GnomAD3 genomes AF: 0.718 AC: 109125 AN: 151884 Hom.: 39349 Cov.: 33

Gnomad AFR AF: 0.670

Gnomad AMI AF: 0.733

Gnomad AMR AF: 0.747

Gnomad ASJ AF: 0.609

Gnomad EAS AF: 0.745

Gnomad SAS AF: 0.727

Gnomad FIN AF: 0.733

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.743

Gnomad OTH AF: 0.694

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

GnomAD4 genome AF: 0.718 AC: 109195 AN: 152002 Hom.: 39371 Cov.: 33 AF XY: 0.719 AC XY: 53369 AN XY: 74276

Gnomad4 AFR AF: 0.670

Gnomad4 AMR AF: 0.748

Gnomad4 ASJ AF: 0.609

Gnomad4 EAS AF: 0.745

Gnomad4 SAS AF: 0.726

Gnomad4 FIN AF: 0.733

Gnomad4 NFE AF: 0.743

Gnomad4 OTH AF: 0.694

Alfa AF: 0.728 Hom.: 39999

Bravo AF: 0.717

Asia WGS AF: 0.704 AC: 2447 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	5.3
DANN	Benign	0.82

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: rs1899979; hg19: chr10-60580635;