NM_001378074.1:c.-82+13112C>T

Variant names:

• chr3-113229386-C-T
• rs931701
• NM_001378074.1:c.-82+13112C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 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=-0.87).
• 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 rank	MANE	Protein	UniProt
BOC	NM_001378074.1	c.-82+13112C>T		intron_variant	Intron 2 of 19	ENST00000682979.1	NP_001365003.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BOC	ENST00000682979.1	c.-82+13112C>T		intron_variant	Intron 2 of 19		NM_001378074.1	ENSP00000507783.1

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

African (AFR) AF: 0.0241 AC: 1003 AN: 41552

American (AMR) AF: 0.242 AC: 3695 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.129 AC: 446 AN: 3464

East Asian (EAS) AF: 0.383 AC: 1978 AN: 5164

South Asian (SAS) AF: 0.244 AC: 1177 AN: 4824

European-Finnish (FIN) AF: 0.134 AC: 1415 AN: 10578

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.0961 AC: 6536 AN: 67996

Other (OTH) AF: 0.120 AC: 252 AN: 2108

Alfa AF: 0.0976 Hom.: 669

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
PhyloP100		-1.1
Mutation Taster		=99/1	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: rs931701; hg19: chr3-112948233; COSMIC: COSV56351324;