chr3-113276227-A-C

Variant names:

• chr3-113276227-A-C
• rs775227
• NM_001378074.1:c.1542+1545A>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 9 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001378074.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BOC	NM_001378074.1	MANE Select	c.1542+1545A>C		intron	N/A	NP_001365003.1	Q9BWV1-3
	BOC	NM_001301861.2		c.1542+1545A>C		intron	N/A	NP_001288790.1	Q9BWV1-3
	BOC	NM_001378073.1		c.1542+1545A>C		intron	N/A	NP_001365002.1	Q9BWV1-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BOC	ENST00000682979.1	MANE Select	c.1542+1545A>C		intron	N/A	ENSP00000507783.1	Q9BWV1-3
	BOC	ENST00000273395.8	TSL:1	c.1542+1545A>C		intron	N/A	ENSP00000273395.4	Q9BWV1-3
	BOC	ENST00000495514.5	TSL:1	c.1542+1545A>C		intron	N/A	ENSP00000418663.1	Q9BWV1-1

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

African (AFR) AF: 0.306 AC: 12704 AN: 41508

American (AMR) AF: 0.140 AC: 2144 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.169 AC: 588 AN: 3472

East Asian (EAS) AF: 0.146 AC: 756 AN: 5186

South Asian (SAS) AF: 0.128 AC: 618 AN: 4826

European-Finnish (FIN) AF: 0.115 AC: 1225 AN: 10616

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.184 AC: 12508 AN: 68014

Other (OTH) AF: 0.188 AC: 397 AN: 2114

Alfa AF: 0.199 Hom.: 3089

Bravo AF: 0.212

Asia WGS AF: 0.126 AC: 440 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	8.4
DANN	Benign	0.58
PhyloP100		1.6
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs775227; hg19: chr3-112995074;