rs150875611

Variant names:

• chr3-113268304-C-A
• rs150875611
• NM_001378074.1:c.382C>A

Your query was ambiguous. Multiple possible variants found:

• chr3-113268304-C-A
• chr3-113268304-C-G
• chr3-113268304-C-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.382C>A​(p.Gln128Lys) 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. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. Q128E) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 32)
• Consequence: BOC NM_001378074.1 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.82

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]

LOC124909409 (HGNC:):

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=0.12584451).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BOC	NM_001378074.1	c.382C>A	p.Gln128Lys	missense_variant	Exon 5 of 20	ENST00000682979.1	NP_001365003.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BOC	ENST00000682979.1	c.382C>A	p.Gln128Lys	missense_variant	Exon 5 of 20		NM_001378074.1	ENSP00000507783.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.099
BayesDel_addAF	Benign	-0.18	T
BayesDel_noAF	Benign	-0.50
CADD	Benign	19
DANN	Benign	0.62
DEOGEN2	Benign	0.29	T;.;.;T
Eigen	Benign	-0.67
Eigen_PC	Benign	-0.45
FATHMM_MKL	Uncertain	0.94	D
LIST_S2	Benign	0.73	.;T;T;T
M_CAP	Benign	0.012	T
MetaRNN	Benign	0.13	T;T;T;T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	1.3	L;.;L;L
PrimateAI	Benign	0.43	T
PROVEAN	Benign	-0.22	N;N;N;N
REVEL	Benign	0.083
Sift	Benign	0.62	T;T;T;T
Sift4G	Benign	0.92	T;T;T;T
Polyphen		0.0	B;.;B;B
Vest4		0.12
MutPred		0.38		Gain of ubiquitination at Q128 (P = 0.0388);.;Gain of ubiquitination at Q128 (P = 0.0388);Gain of ubiquitination at Q128 (P = 0.0388);
MVP		0.59
MPC		0.29
ClinPred		0.64	D
GERP RS		4.7
Varity_R		0.12
gMVP		0.58

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: rs150875611; hg19: chr3-112987151;