10-58512948-T-C

Position:

• chr10-58512948-T-C

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.-196T>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.511 in 146,672 control chromosomes in the GnomAD database, including 19,538 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.51 (19538 hom., cov: 32)
• Consequence: BICC1 NM_001080512.3 5_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -2.02

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=-0.56).
• BP6: Variant 10-58512948-T-C is Benign according to our data. Variant chr10-58512948-T-C is described in ClinVar as [Benign]. Clinvar id is 1223334.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.601 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BICC1	NM_001080512.3	c.-196T>C		5_prime_UTR_variant	1/21	ENST00000373886.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BICC1	ENST00000373886.8	c.-196T>C		5_prime_UTR_variant	1/21	1	NM_001080512.3	P1

Frequencies

GnomAD3 genomes AF: 0.510 AC: 74814 AN: 146564 Hom.: 19509 Cov.: 32

Gnomad AFR AF: 0.607

Gnomad AMI AF: 0.334

Gnomad AMR AF: 0.369

Gnomad ASJ AF: 0.503

Gnomad EAS AF: 0.466

Gnomad SAS AF: 0.562

Gnomad FIN AF: 0.542

Gnomad MID AF: 0.542

Gnomad NFE AF: 0.481

Gnomad OTH AF: 0.514

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

GnomAD4 genome AF: 0.511 AC: 74883 AN: 146672 Hom.: 19538 Cov.: 32 AF XY: 0.513 AC XY: 36613 AN XY: 71396

Gnomad4 AFR AF: 0.607

Gnomad4 AMR AF: 0.368

Gnomad4 ASJ AF: 0.503

Gnomad4 EAS AF: 0.466

Gnomad4 SAS AF: 0.562

Gnomad4 FIN AF: 0.542

Gnomad4 NFE AF: 0.481

Gnomad4 OTH AF: 0.519

Alfa AF: 0.362 Hom.: 913

Bravo AF: 0.492

Asia WGS AF: 0.495 AC: 1264 AN: 2562

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 10, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
CADD	Benign	14
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs112597538; hg19: chr10-60272708;