3-113254270-A-G

Variant names:

• chr3-113254270-A-G
• rs775219
• NM_001378074.1:c.376+3437A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 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 -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.

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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BOC	NM_001378074.1	MANE Select	c.376+3437A>G		intron	N/A	NP_001365003.1
	BOC	NM_001301861.2		c.376+3437A>G		intron	N/A	NP_001288790.1
	BOC	NM_001378073.1		c.376+3437A>G		intron	N/A	NP_001365002.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BOC	ENST00000682979.1	MANE Select	c.376+3437A>G		intron	N/A	ENSP00000507783.1
	BOC	ENST00000273395.8	TSL:1	c.376+3437A>G		intron	N/A	ENSP00000273395.4
	BOC	ENST00000495514.5	TSL:1	c.376+3437A>G		intron	N/A	ENSP00000418663.1

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

African (AFR) AF: 0.658 AC: 27274 AN: 41426

American (AMR) AF: 0.445 AC: 6805 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.300 AC: 1043 AN: 3472

East Asian (EAS) AF: 0.592 AC: 3056 AN: 5158

South Asian (SAS) AF: 0.402 AC: 1935 AN: 4808

European-Finnish (FIN) AF: 0.468 AC: 4942 AN: 10570

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.285 AC: 19361 AN: 67974

Other (OTH) AF: 0.394 AC: 828 AN: 2104

Alfa AF: 0.335 Hom.: 4397

Bravo AF: 0.439

Asia WGS AF: 0.483 AC: 1681 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.40
CADD	Benign	11
DANN	Benign	0.74
PhyloP100		1.2
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: rs775219; hg19: chr3-112973117; COSMIC: COSV56357669; COSMIC: COSV56357669;