3-113259917-T-C

Variant names:

• chr3-113259917-T-C
• rs1875111
• NM_001378074.1:c.377-8382T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001378074.1(BOC):​c.377-8382T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.35 in 151,960 control chromosomes in the GnomAD database, including 10,355 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 0.35 (10355 hom., cov: 32)
• Consequence: BOC NM_001378074.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.675
• Publications: 3 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]

ENSG00000288079 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.493 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BOC	NM_001378074.1	c.377-8382T>C		intron_variant	Intron 4 of 19	ENST00000682979.1	NP_001365003.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BOC	ENST00000682979.1	c.377-8382T>C		intron_variant	Intron 4 of 19		NM_001378074.1	ENSP00000507783.1

Frequencies

GnomAD3 genomes AF: 0.350 AC: 53154 AN: 151842 Hom.: 10321 Cov.: 32

Gnomad AFR AF: 0.484

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.415

Gnomad ASJ AF: 0.240

Gnomad EAS AF: 0.509

Gnomad SAS AF: 0.360

Gnomad FIN AF: 0.366

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.249

Gnomad OTH AF: 0.324

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

GnomAD4 genome AF: 0.350 AC: 53232 AN: 151960 Hom.: 10355 Cov.: 32 AF XY: 0.358 AC XY: 26613 AN XY: 74288

African (AFR) AF: 0.484 AC: 20043 AN: 41412

American (AMR) AF: 0.416 AC: 6345 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.240 AC: 831 AN: 3468

East Asian (EAS) AF: 0.510 AC: 2627 AN: 5154

South Asian (SAS) AF: 0.360 AC: 1731 AN: 4812

European-Finnish (FIN) AF: 0.366 AC: 3867 AN: 10558

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.249 AC: 16910 AN: 67978

Other (OTH) AF: 0.321 AC: 677 AN: 2110

Alfa AF: 0.283 Hom.: 17470

Bravo AF: 0.360

Asia WGS AF: 0.417 AC: 1450 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.1
DANN	Benign	0.32
PhyloP100		-0.68
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: rs1875111; hg19: chr3-112978764;