rs775219

chr3-113254270-A-Gchr3-113254270-A-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_001378074.1(BOC):c.376+3437A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.431 in 152,002 control chromosomes in the GnomAD database, including 16,177 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 0.43 (16177 hom., cov: 32)
• Consequence: BOC NM_001378074.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.24

Genes affected

BOC (HGNC:17173): (BOC cell adhesion associated, oncogene regulated) The protein encoded by this gene is a member of the immunoglobulin/fibronectin type III repeat family. It is a component of a cell-surface receptor complex that mediates cell-cell interactions between muscle precursor cells, and promotes myogenic differentiation. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Sep 2014]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.4).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.652 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BOC	NM_001378074.1	c.376+3437A>G		intron_variant		ENST00000682979.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BOC	ENST00000682979.1	c.376+3437A>G		intron_variant			NM_001378074.1	A2

Frequencies

GnomAD3 genomes AF: 0.430 AC: 65364 AN: 151884 Hom.: 16131 Cov.: 32

Gnomad AFR AF: 0.658

Gnomad AMI AF: 0.141

Gnomad AMR AF: 0.445

Gnomad ASJ AF: 0.300

Gnomad EAS AF: 0.592

Gnomad SAS AF: 0.403

Gnomad FIN AF: 0.468

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.285

Gnomad OTH AF: 0.397

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

GnomAD4 genome AF: 0.431 AC: 65458 AN: 152002 Hom.: 16177 Cov.: 32 AF XY: 0.439 AC XY: 32622 AN XY: 74294

Gnomad4 AFR AF: 0.658

Gnomad4 AMR AF: 0.445

Gnomad4 ASJ AF: 0.300

Gnomad4 EAS AF: 0.592

Gnomad4 SAS AF: 0.402

Gnomad4 FIN AF: 0.468

Gnomad4 NFE AF: 0.285

Gnomad4 OTH AF: 0.394

Alfa AF: 0.357 Hom.: 2812

Bravo AF: 0.439

Asia WGS AF: 0.483 AC: 1681 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.40
Cadd	Benign	11
Dann	Benign	0.74

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: rs775219; hg19: chr3-112973117; COSMIC: COSV56357669; COSMIC: COSV56357669;