Variant rs775219 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The NM_001378074.1(BOC):c.376+3437A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.431 in 152,002 control chromosomes in the GnomAD database, including 16,177 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 0.43 ( 16177 hom., cov: 32)

Consequence

BOC
NM_001378074.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.24

Variant links:

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]

BOC links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.4).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.652 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BOC	NM_001378074.1 linkuse as main transcript	c.376+3437A>G		intron_variant		ENST00000682979.1	NP_001365003.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BOC	ENST00000682979.1 linkuse as main transcript	c.376+3437A>G		intron_variant			NM_001378074.1	ENSP00000507783	A2	Q9BWV1-3

Frequencies

GnomAD3 genomes

AF:

0.430

AC:

65364

AN:

151884

Hom.:

16131

Cov.:

show subpopulations

Gnomad AFR

AF:

0.658

Gnomad AMI

AF:

0.141

Gnomad AMR

AF:

0.445

Gnomad ASJ

AF:

0.300

Gnomad EAS

AF:

0.592

Gnomad SAS

AF:

0.403

Gnomad FIN

AF:

0.468

Gnomad MID

AF:

0.291

Gnomad NFE

AF:

0.285

Gnomad OTH

AF:

0.397

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

GnomAD4 genome

AF:

0.431

AC:

65458

AN:

152002

Hom.:

16177

Cov.:

AF XY:

0.439

AC XY:

32622

AN XY:

74294

show subpopulations

Gnomad4 AFR

AF:

0.658

Gnomad4 AMR

AF:

0.445

Gnomad4 ASJ

AF:

0.300

Gnomad4 EAS

AF:

0.592

Gnomad4 SAS

AF:

0.402

Gnomad4 FIN

AF:

0.468

Gnomad4 NFE

AF:

0.285

Gnomad4 OTH

AF:

0.394

Alfa

AF:

0.357

Hom.:

2812

Bravo

AF:

0.439

Asia WGS

AF:

0.483

AC:

1681

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.40

CADD

Benign

DANN

Benign

0.74

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over