10-58513093-G-A

Position:

• chr10-58513093-G-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_001080512.3(BICC1):​c.-51G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00505 in 1,308,536 control chromosomes in the GnomAD database, including 286 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.026 (177 hom., cov: 33)
  • Exomes 𝑓: 0.0023 (109 hom.)
• Consequence: BICC1 NM_001080512.3 5_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 2.43

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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.55).
• BP6: Variant 10-58513093-G-A is Benign according to our data. Variant chr10-58513093-G-A is described in ClinVar as [Benign]. Clinvar id is 1274741.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0874 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BICC1	NM_001080512.3	c.-51G>A		5_prime_UTR_variant	1/21	ENST00000373886.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BICC1	ENST00000373886.8	c.-51G>A		5_prime_UTR_variant	1/21	1	NM_001080512.3	P1

Frequencies

GnomAD3 genomes AF: 0.0257 AC: 3888 AN: 151340 Hom.: 178 Cov.: 33

Gnomad AFR AF: 0.0900

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00678

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000414

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00955

Gnomad NFE AF: 0.000384

Gnomad OTH AF: 0.0169

GnomAD3 exomes AF: 0.000942 AC: 10 AN: 10614 Hom.: 2 AF XY: 0.000654 AC XY: 4 AN XY: 6118

Gnomad AFR exome AF: 0.135

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000286

Gnomad OTH exome AF: 0.00917

GnomAD4 exome AF: 0.00235 AC: 2714 AN: 1157090 Hom.: 109 Cov.: 21 AF XY: 0.00210 AC XY: 1180 AN XY: 560690

Gnomad4 AFR exome AF: 0.0924

Gnomad4 AMR exome AF: 0.00622

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000498

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.000260

Gnomad4 OTH exome AF: 0.00624

GnomAD4 genome AF: 0.0257 AC: 3890 AN: 151446 Hom.: 177 Cov.: 33 AF XY: 0.0248 AC XY: 1834 AN XY: 74022

Gnomad4 AFR AF: 0.0898

Gnomad4 AMR AF: 0.00677

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000414

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000384

Gnomad4 OTH AF: 0.0167

Alfa AF: 0.0208 Hom.: 9

Bravo AF: 0.0288

Asia WGS AF: 0.00524 AC: 18 AN: 3450

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 02, 2020

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.55
CADD	Benign	15
DANN	Uncertain	0.98

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs184291321; hg19: chr10-60272853;