chr3-113250569-G-T

Position:

• chr3-113250569-G-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001378074.1(BOC):​c.112G>T​(p.Val38Phe) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: BOC NM_001378074.1 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 6.84

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 Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.1607134).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BOC	NM_001378074.1	c.112G>T	p.Val38Phe	missense_variant	4/20	ENST00000682979.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BOC	ENST00000682979.1	c.112G>T	p.Val38Phe	missense_variant	4/20		NM_001378074.1	A2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Sep 27, 2021

The c.112G>T (p.V38F) alteration is located in exon 4 (coding exon 2) of the BOC gene. This alteration results from a G to T substitution at nucleotide position 112, causing the valine (V) at amino acid position 38 to be replaced by a phenylalanine (F). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.41
BayesDel_addAF	Uncertain	0.014	T
BayesDel_noAF	Benign	-0.22
CADD	Benign	21
DANN	Benign	0.87
DEOGEN2	Benign	0.21	.;T;T;.;T;T
Eigen	Benign	-0.23
Eigen_PC	Benign	0.066
FATHMM_MKL	Uncertain	0.90	D
LIST_S2	Uncertain	0.88	D;.;.;D;D;D
M_CAP	Benign	0.038	D
MetaRNN	Benign	0.16	T;T;T;T;T;T
MetaSVM	Benign	-0.71	T
MutationAssessor	Benign	-1.1	.;N;.;N;N;.
MutationTaster	Benign	1.0	D;D;D;D;D
PrimateAI	Uncertain	0.50	T
PROVEAN	Benign	1.4	N;N;N;N;N;N
REVEL	Benign	0.23
Sift	Benign	0.53	T;T;T;T;T;T
Sift4G	Pathogenic	0.0	D;T;D;T;T;D
Polyphen		0.72	P;B;B;B;B;B
Vest4		0.36, 0.21, 0.37, 0.37, 0.22
MutPred		0.49		Loss of glycosylation at T39 (P = 0.0916);Loss of glycosylation at T39 (P = 0.0916);Loss of glycosylation at T39 (P = 0.0916);Loss of glycosylation at T39 (P = 0.0916);Loss of glycosylation at T39 (P = 0.0916);Loss of glycosylation at T39 (P = 0.0916);
MVP		0.84
MPC		0.33
ClinPred		0.80	D
GERP RS		5.7
Varity_R		0.19
gMVP		0.72

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr3-112969416;