chr3-113229386-C-T

Position:

• chr3-113229386-C-T

Variant summary

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

The NM_001378074.1(BOC):​c.-82+13112C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.109 in 152,186 control chromosomes in the GnomAD database, including 1,540 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 0.11 (1540 hom., cov: 32)
• Consequence: BOC NM_001378074.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05

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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.369 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BOC	NM_001378074.1	c.-82+13112C>T		intron_variant		ENST00000682979.1	NP_001365003.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BOC	ENST00000682979.1	c.-82+13112C>T		intron_variant			NM_001378074.1	ENSP00000507783	A2

Frequencies

GnomAD3 genomes AF: 0.109 AC: 16565 AN: 152068 Hom.: 1533 Cov.: 32

Gnomad AFR AF: 0.0242

Gnomad AMI AF: 0.0493

Gnomad AMR AF: 0.241

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.384

Gnomad SAS AF: 0.244

Gnomad FIN AF: 0.134

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0962

Gnomad OTH AF: 0.119

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

GnomAD4 genome AF: 0.109 AC: 16573 AN: 152186 Hom.: 1540 Cov.: 32 AF XY: 0.119 AC XY: 8814 AN XY: 74374

Gnomad4 AFR AF: 0.0241

Gnomad4 AMR AF: 0.242

Gnomad4 ASJ AF: 0.129

Gnomad4 EAS AF: 0.383

Gnomad4 SAS AF: 0.244

Gnomad4 FIN AF: 0.134

Gnomad4 NFE AF: 0.0961

Gnomad4 OTH AF: 0.120

Alfa AF: 0.105 Hom.: 353

Bravo AF: 0.112

Asia WGS AF: 0.261 AC: 907 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.5
DANN	Benign	0.60

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: rs931701; hg19: chr3-112948233; COSMIC: COSV56351324;