rs775227

Positions:

• chr3-113276227-A-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001378074.1(BOC):​c.1542+1545A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.205 in 152,238 control chromosomes in the GnomAD database, including 3,508 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 0.20 (3508 hom., cov: 33)
• Consequence: BOC NM_001378074.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.63

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.302 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BOC	NM_001378074.1	c.1542+1545A>C		intron_variant		ENST00000682979.1	NP_001365003.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BOC	ENST00000682979.1	c.1542+1545A>C		intron_variant			NM_001378074.1	ENSP00000507783	A2

Frequencies

GnomAD3 genomes AF: 0.205 AC: 31125 AN: 152120 Hom.: 3501 Cov.: 33

Gnomad AFR AF: 0.306

Gnomad AMI AF: 0.180

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.169

Gnomad EAS AF: 0.146

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.115

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.184

Gnomad OTH AF: 0.192

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

GnomAD4 genome AF: 0.205 AC: 31159 AN: 152238 Hom.: 3508 Cov.: 33 AF XY: 0.200 AC XY: 14863 AN XY: 74424

Gnomad4 AFR AF: 0.306

Gnomad4 AMR AF: 0.140

Gnomad4 ASJ AF: 0.169

Gnomad4 EAS AF: 0.146

Gnomad4 SAS AF: 0.128

Gnomad4 FIN AF: 0.115

Gnomad4 NFE AF: 0.184

Gnomad4 OTH AF: 0.188

Alfa AF: 0.185 Hom.: 1308

Bravo AF: 0.212

Asia WGS AF: 0.126 AC: 440 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	8.4
DANN	Benign	0.58

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: rs775227; hg19: chr3-112995074;