10-58513361-T-C

Position:

• chr10-58513361-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.190+28T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.478 in 1,555,464 control chromosomes in the GnomAD database, including 180,619 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.51 (20243 hom., cov: 33)
  • Exomes 𝑓: 0.47 (160376 hom.)
• Consequence: BICC1 NM_001080512.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.570

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=-0.84).
• BP6: Variant 10-58513361-T-C is Benign according to our data. Variant chr10-58513361-T-C is described in ClinVar as [Benign]. Clinvar id is 1280720.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.6 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BICC1	NM_001080512.3	c.190+28T>C		intron_variant		ENST00000373886.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BICC1	ENST00000373886.8	c.190+28T>C		intron_variant		1	NM_001080512.3	P1

Frequencies

GnomAD3 genomes AF: 0.510 AC: 77485 AN: 151904 Hom.: 20211 Cov.: 33

Gnomad AFR AF: 0.606

Gnomad AMI AF: 0.333

Gnomad AMR AF: 0.367

Gnomad ASJ AF: 0.503

Gnomad EAS AF: 0.462

Gnomad SAS AF: 0.561

Gnomad FIN AF: 0.548

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.480

Gnomad OTH AF: 0.514

GnomAD3 exomes AF: 0.480 AC: 101793 AN: 212114 Hom.: 25355 AF XY: 0.489 AC XY: 56843 AN XY: 116152

Gnomad AFR exome AF: 0.619

Gnomad AMR exome AF: 0.274

Gnomad ASJ exome AF: 0.522

Gnomad EAS exome AF: 0.466

Gnomad SAS exome AF: 0.578

Gnomad FIN exome AF: 0.552

Gnomad NFE exome AF: 0.478

Gnomad OTH exome AF: 0.451

GnomAD4 exome AF: 0.475 AC: 666073 AN: 1403442 Hom.: 160376 Cov.: 30 AF XY: 0.479 AC XY: 332790 AN XY: 694872

Gnomad4 AFR exome AF: 0.624

Gnomad4 AMR exome AF: 0.289

Gnomad4 ASJ exome AF: 0.506

Gnomad4 EAS exome AF: 0.490

Gnomad4 SAS exome AF: 0.578

Gnomad4 FIN exome AF: 0.550

Gnomad4 NFE exome AF: 0.464

Gnomad4 OTH exome AF: 0.488

GnomAD4 genome AF: 0.510 AC: 77560 AN: 152022 Hom.: 20243 Cov.: 33 AF XY: 0.512 AC XY: 38073 AN XY: 74296

Gnomad4 AFR AF: 0.606

Gnomad4 AMR AF: 0.366

Gnomad4 ASJ AF: 0.503

Gnomad4 EAS AF: 0.462

Gnomad4 SAS AF: 0.561

Gnomad4 FIN AF: 0.548

Gnomad4 NFE AF: 0.480

Gnomad4 OTH AF: 0.518

Alfa AF: 0.492 Hom.: 4947

Bravo AF: 0.493

Asia WGS AF: 0.558 AC: 1939 AN: 3478

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	-0.84
CADD	Benign	3.5
DANN	Benign	0.31

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: rs7100474; hg19: chr10-60273121; COSMIC: COSV65857688;