chr10-58513395-C-A

Position:

• chr10-58513395-C-A

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_001080512.3(BICC1):​c.190+62C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.479 in 1,438,154 control chromosomes in the GnomAD database, including 166,943 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.51 (20202 hom., cov: 33)
  • Exomes 𝑓: 0.47 (146741 hom.)
• Consequence: BICC1 NM_001080512.3 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 0.0160

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 -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BP6: Variant 10-58513395-C-A is Benign according to our data. Variant chr10-58513395-C-A is described in ClinVar as [Benign]. Clinvar id is 1261535.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 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+62C>A		intron_variant		ENST00000373886.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BICC1	ENST00000373886.8	c.190+62C>A		intron_variant		1	NM_001080512.3	P1

Frequencies

GnomAD3 genomes AF: 0.510 AC: 77425 AN: 151892 Hom.: 20170 Cov.: 33

Gnomad AFR AF: 0.606

Gnomad AMI AF: 0.330

Gnomad AMR AF: 0.366

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

GnomAD4 exome AF: 0.475 AC: 610826 AN: 1286144 Hom.: 146741 AF XY: 0.479 AC XY: 302005 AN XY: 630948

Gnomad4 AFR exome AF: 0.624

Gnomad4 AMR exome AF: 0.305

Gnomad4 ASJ exome AF: 0.507

Gnomad4 EAS exome AF: 0.492

Gnomad4 SAS exome AF: 0.581

Gnomad4 FIN exome AF: 0.552

Gnomad4 NFE exome AF: 0.463

Gnomad4 OTH exome AF: 0.488

GnomAD4 genome AF: 0.510 AC: 77500 AN: 152010 Hom.: 20202 Cov.: 33 AF XY: 0.512 AC XY: 38048 AN XY: 74300

Gnomad4 AFR AF: 0.606

Gnomad4 AMR AF: 0.365

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: 0.505 Hom.: 4297

Bravo AF: 0.493

Asia WGS AF: 0.556 AC: 1933 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
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	-0.74
CADD	Benign	10
DANN	Benign	0.65

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: rs7079648; hg19: chr10-60273155; COSMIC: COSV65857690;