10-58755262-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.308-29739T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.524 in 151,938 control chromosomes in the GnomAD database, including 21,081 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 0.52 (21081 hom., cov: 32)
• Consequence: BICC1 NM_001080512.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.184

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=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.615 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BICC1	NM_001080512.3	c.308-29739T>C		intron_variant		ENST00000373886.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BICC1	ENST00000373886.8	c.308-29739T>C		intron_variant		1	NM_001080512.3	P1

Frequencies

GnomAD3 genomes AF: 0.524 AC: 79599 AN: 151822 Hom.: 21066 Cov.: 32

Gnomad AFR AF: 0.470

Gnomad AMI AF: 0.633

Gnomad AMR AF: 0.625

Gnomad ASJ AF: 0.625

Gnomad EAS AF: 0.551

Gnomad SAS AF: 0.496

Gnomad FIN AF: 0.446

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.540

Gnomad OTH AF: 0.536

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

GnomAD4 genome AF: 0.524 AC: 79643 AN: 151938 Hom.: 21081 Cov.: 32 AF XY: 0.520 AC XY: 38608 AN XY: 74274

Gnomad4 AFR AF: 0.469

Gnomad4 AMR AF: 0.625

Gnomad4 ASJ AF: 0.625

Gnomad4 EAS AF: 0.550

Gnomad4 SAS AF: 0.496

Gnomad4 FIN AF: 0.446

Gnomad4 NFE AF: 0.540

Gnomad4 OTH AF: 0.532

Alfa AF: 0.521 Hom.: 11155

Bravo AF: 0.539

Asia WGS AF: 0.514 AC: 1786 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	0.56
Dann	Benign	0.50

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: rs7094271; hg19: chr10-60515022;